Evangelion Gear
by Snafu the Great
Summary: NGE/MGS fusion. Big Boss takes Shinji as his student. Unknown to Shinji, Big Boss is also opposing both Seele and Gendou's plans to unleash Third Impact, and intends to stop them both. Story complete.
1. Prologue: The Story So Far

**Evangelion Gear**  
A Neon Genesis Evangelion/Metal Gear fusion  
By Snafu the Great

Snafu's Disclaimer: I seriously doubt that Hideaki Anno, GAINAX, Konami, Fox Productions and Hideo Kojima himself would get a pound of flesh from my hide for using their characters, but better safe than sorry. Evangelion and Metal Gear are the property of their respective owners. Yours Truly is just simply just borrowing them for my first sortie into both Evangelion and Metal Gear. Now being a big fan of Metal Gear, I was kinda disappointed as to how they did Solid Snake in the game, so I've taken several liberties with the storyline, as well as with several other characters, Shinji included. Oh, yes, Shinji Ikari will be very OOC for this story, but for good reason. Reason being is that he grows a pair of balls.

UPDATE: I fixed one major part in the timeline. Big Boss and Snake meet up in 2012, at the same time Seele attacks the Patriots.

UPDATE Pt. 2: Parts of the story have been fixed. Originally, I was going to introduce the Beauty and Beast Unit in Episode 5, but I couldn't figure out how to do so. Instead, they are introduced in Episode 3. Oh, and I fixed the dates for the Metal Gear-related stuff.

UPDATE Pt. 3: Grammar errors cleaned up. Also added some more bits and pieces from both Metal Gear and Evangelion to the timeline. And I fixed the Evangelion-related dates for the timeline, after someone pointed out the errors. Also, John Hayter is not Big Boss' real name. I simply combined his first name with the last name of the guy who does the voice (David Hayter). There's also a friendly jab to both Kojima and Anno in the timeline as well.

Before you begin reading, here are the major changes I mentioned:

1. Snake does not have that pesky accelerated aging seen in MGS4, and he is cured of FOXDIE. Nor does Naomi have terminal cancer.  
2. Vamp is permanently dead. Sorry Vamp fans.  
3. No Gekko, no PMCs...well, I might throw in a PMC, but they will be on Seele's payroll.  
4. Raiden is still human, and still with Rose. The couple have adopted Sunny shortly after the Manhattan fiasco. They still have their kid too.

Okay, that about covers it. The story takes place after Zeruel's assault on the Geofront. On with the story!

_**Prologue: The Story So Far...**_

**The History of EVANGELION GEAR**

About 4.5 billion years ago: The Giant of Light, codenamed ADAM (progenitor of the Angels), arrives on Earth in present-day Antarctica via the White Moon. An unknown period of time later, the second Seed of Life, codenamed Lilith (progenitor of humanity), arrives on Earth when her Black Moon crashes on Earth in present-day Japan, thus creating the Moon from the Earth's fragments. This event is called **First Impact**.

1909, August 12: David Oh, alias Major Zero, is born.

1922: The Boss (real name, unknown) is born.

1935: John Hayter alias, Naked Snake and later, Big Boss, is born.

1936, May 15: Tatyana, alias EVA, is born.

1944, D-Day: Adamska, alias Revolver Ocelot, is born to The Boss and The Sorrow in the midst of Omaha Beach in Normandy.

1947: The Dead Sea Scrolls are discovered in a cave near the Dead Sea in Israel. Within the scrolls is a hidden segment of the scrolls, which tells the coming of the Angels, the Evangelions, Third Impact and many more events to come. The mysterious entity known as Seele acquires the Secret Dead Sea Scrolls (also known as the War Scrolls), and plans on triggering Third Impact to evolve humanity further, as they believe that humanity is currently stagnating.

1955, April 9: Kouzou Fuyutsuki is born.

1960, May 22: Hideaki Anno is born.

1963, August 24: Hideo Kojima is born.

1964, August 24: **Virtuous Mission**. FOX (Force Operations X) operative codenamed Naked Snake is sent into the Soviet Union to rescue Soviet designer Nikolai Sokolov. The mission is a failure when Cobra Unit, led by The Boss, defects to the Soviet Union.

August 30 to September 2: **Operation Snake Eater**. Naked Snake is sent back into Russia. The mission is a success. The Cobra Unit, as well as The Boss and Red Army Colonel Yevgeny Borisovitch Volgin is killed. Naked Snake is awarded the title 'Big Boss.'

1967, April 29: Gendou Rokubungi is born.

1970: The Patriots are formed. Its original purpose is to reform the world as The Boss envisioned it – a world united. Its members include its founder, Major Zero, Ocelot, Para-Medic (Dr. Clark), Signt (Donald Anderson), and Big Boss. EVA will be the last person to join the organization at Big Boss' request. However, as time passes, Major Zero, Para-Medic, and Signt becomes corrupt with power.

1971: Big Boss establishes the Special Forces black-ops unit FOXHOUND, with himself as its commanding officer.

1973: Les Infant Terribles (The Terrible Infants) Project. Using genetic material from Big Boss, combined with the eggs of Dr. Clark's Japanese assistant (with EVA carrying the babies full-term), the 'sons' of Big Boss - Solid, Liquid, and Solidus Snake - are born. As a result of this betrayal, Big Boss leaves The Patriots and travels the world as a mercenary.

1977, March 30: Yui Ikari is born. Her father sits on the council of Seele.

Sometime in the 1980s, exact date unknown: Big Boss establishes Outer Heaven, a mercenary-state for soldiers. During this time, Big Boss also fights in several civil wars on the African continent as a mercenary.

1985, June 17: Ryouji Kaji is born.

November 21: Ritsuko Akagi is born.

1986, December 8: Misato Katsuragi is born.

1987, December 8: Meryl Silverburgh is born, the product of an affair between Roy Campbell (her uncle) and her mother.

1989: Big Boss resumes command of FOXHOUND.

1990: Solid Snake joins the U.S. Army, and is recruited into the Green Berets. He sees action in the Gulf War.

1995: Solid Snake is recruited into FOXHOUND. He does not know about his connection to his commanding officer, Big Boss.

**Outer Heaven Incident**. Big Boss makes his bid for power. Using Metal Gear, a walking battle tank with nuclear capabilities, he plans on overthrowing Zero and the Patriots. However, Zero and Signt (Donald Anderson) trick Solid Snake into infiltrating Outer Heaven. Snake is successful in his mission by defeating Big Boss and destroying Metal Gear.

1999: Christmas Eve – **Zanzibarland Disturbance**. Solid Snake is brought out of retirement in order to infiltrate Zanzibarland and rescue OLIX creator Dr. Kilo Marx. Marx dies in the rescue attempt, but Snake is successful in retrieving the OLIX schematics. He also puts a stop to Big Boss' intentions by defeating both Gray Fox and Big Boss. What Solid Snake (nor the Patriots) does not know is that the man thought to have been Big Boss is in fact a decoy. The real Big Boss is in fact, has been recovering in Japan since Outer Heaven. Solid Snake returns to Alaska.

Early 2000: Construction of the Patriots' neural AIs (codenamed GW,TJ, AL, TR, and JD) begins. Zero gives Signt (Donald Anderson) the order to construct the AIs, given his lack of trust in humanity.

Mid 2000: Katsuragi Research Expedition. Led by renowned scientist Hideaki Katsuragi, the expedition is in Antarctica to research ADAM, hidden under Mt. Markham. Among those present are Seele Chairman Keel Lorenz, researcher Gendou Rokubungi, and Doctor Katsuragi's 14-year-old daughter, Misato.

13 September 2000: The cataclysmic event known as **Second Impact **takes place. The official story is that a meteorite traveling at light speed crashed into the South Pole, thus melting the ice caps, triggering mega tsunamis that wipe out 2 billion people in the Southern Hemisphere. However, the truth is far worse. On Seele's orders, Gendou Rokubungi sabotaged Katsuragi's Contact Experiment with ADAM the previous day, and then departed for Japan. Out of the entire Katsuragi Expedition, only Dr. Katsuragi's daughter, Misato, survives. As a result of this catastrophe, the Earth's axis has shifted, reducing the seasons to a permanent summer. The ensuing wars claim an additional billion lives, bringing the death toll to three billion.

Kaworu Nagisa, codenamed Tabris, the Angel of Free Will, is born.

22 September 2000: Old Tokyo is destroyed by a nuclear bomb. Among the dead are Johnny Sasaki, and the leader of the Patriots, Major Zero.

14 February 2001: The Valentine Treaty is signed, ending the wars that erupted following Second Impact.

June 6: Shinji Ikari is born to Gendou (formerly Rokubungi) and Yui Ikari.

December 4: Asuka Langley Sohryuu is born to an American father and a Japanese-German mother.

2003: Constructions of the Evangelions begins.

The JSSDF (Japanese Straegic Self-Defense Force) is formed. The main excuse is that the JSSDF is formed in response of the Sino-Vietnamese War over ownership of the Nansha Islands. Several of the instructors are FOXHOUND, Outer Heaven, and Zanzibarland veterans.

Between 2004 and 2008, exact date unknown: Using the Les Enfant Terribles cloning process, Rei Ayanami is created by combining a minor amount of DNA from Yui Ikari with that of Lilith.

2004: In a 'contact experiment' with Evangelion Unit One, Gehirn researcher Yui Ikari is reported killed. In truth, her soul was simply absorbed into the Evangelion's core, her body dissolved into LCL. She is also privy to the information concerning her husband's role in Second Impact, having secretly found out about it shortly before the experiment. Shortly thereafter, Gendou Ikari abandons his son, Shinji Ikari, leaving him with a teacher.

2005, exact date unknown: Gehirn researcher Kyokou Zeppelin Sohryuu commits suicide following her own 'contact experiment,' as a portion of her soul is absorbed into Evangelion Unit Two.

February – **Shadow Moses Incident**. The nuclear weapons disposal facility on Shadow Moses Island in Alaska is taken over by FOXHOUND and the Genome Army. Led by Liquid Snake, they also take hostages – one of which is DARPA executive (and Patriot member) Donald Anderson (Signt) and ArmsTech President Jim Baker. Solid Snake is once again brought out of retirement to combat the threat. Snake also discovers that the facility is also the testing grounds for Metal Gear REX. With the help of weapons designer Hal 'Otacon' Emmerich, Snake destroys REX; as well as eliminate the renegade FOXHOUND operatives, save for Revolver Ocelot, who escape. Solid Snake, Otacon and Meryl Silverburgh, the sole survivor of the Genome Army, escape the facility. FOXHOUND is disbanded as a result.

Construction of the fortress city known as Tokyo-3 begins. The city is built in the location of the pre-Impact city of Hakone.

2007: August 8 – **Manhattan Tanker Incident**. A Russian mercenary army seize control of the USS Discovery off the coast of Manhattan Island, where the US Marines are preparing to test their own Metal Gear, dubbed RAY. Solid Snake, now a part of the anti-Metal Gear group Philanthropy (along with Otacon), infiltrate the ship. The mission goes FUBAR when Sergei Gurlukovitch and Marine Commandant Scott Dolph are killed and Ocelot escapes with RAY. Solid Snake is framed by the Patriots for the tanker's sinking and goes underground.

2009: April 29 to April 30 – **Big Shell Incident**. The rouge special forces team codenamed Dead Cell, lead by Solidus Snake, take over the Big Shell facility, which is in fact, a front for Arsenal Gear. FOXHOUND operative Raiden is sent in to dispatch Dead Cell and Solidus Snake. Solid Snake comes out of hiding to stop Solidus' plans. Dead Cell is eliminated, while Solidus Snake is killed by Raiden. Emma Emmerich, Otacon's estranged stepsister is also killed.

2010: Gehirn researcher and creator of the MAGI supercomputer Naoko Akagi murders Rei Ayanami (the First) in a jealous rage before committing suicide upon finding out that Gendou Ikari is using her. She then commits suicide by throwing herself upon the MAGI. Gendou covers up the suicide. Officially, Naoko Akagi has died in a car accident. Her daughter, Ritsuko, does not know about her mother's affair with Gendou, nor the truth behind her mother's demise. Following this incident, Seele has Gehirn disbanded and reorganized into the anti-Angel agency, Nerv.

2011: Big Boss, along with Ocelot and EVA, destroy the Patriots' AI computers. The Patriots has now been reformed, this time with Big Boss as the leader, with EVA and Ocelot as his lieutenants. Big Boss recruits Naomi Hunter and his old friend Roy Campbell to his ranks, as well as Ryouji Kaji, whom both Big Boss and EVA rescued as a child following Second Impact. The Patriots acquire a copy of the Secret Dead Sea Scrolls and discovers Seele's intentions, as well as their role regarding Second Impact. After meeting with Kaji, who verified it, as well as Seele's plans for Third Impact, the Patriots decide to oppose Seele.

Through Big Boss, The Boss gains a posthumous pardon once certain events regarding the Virtuous Mission becomes known.

Solid Snake is also given a pardon, along with Hal Emmerich. Neither man does not know that Big Boss was responsible...yet.

Construction on the next-generation Metal Gear RAYs begin in secret on Shadow Moses Island. Despite the financial reserves of the Patriots, only three are constructed due to the time frame.

2013, August 27: EVA, Big Boss and Ocelot confront Solid Snake and Meryl Silverburgh somewhere in Eastern Europe. Big Boss and Solid Snake make their peace after Big Boss and Ocelot explain everything, from their history to Seele's intentions of unleashing a Third Impact. Meryl wants revenge, since Second Impact had killed her mother. Seele, seeing the reformed Patriots as a threat to their plans for Third Impact, attempts to eliminate the Patriots once and for all. A hit squad is sent to Eastern Europe, where the Patriots are located. EVA and former FOXHOUNND commanding officer Colonel Roy Campbell are killed in the attempt. Ocelot goes underground and Big Boss returns to Japan. Both men swear revenge.

2014: Solid Snake assumes control of FOXHOUND, with Meryl Silverburgh as his second-in-command, at the request of Big Boss. Hal Emmerich also works for the unit, as does Raiden and Mei Ling. Using a contact within the Japanese Strategic Self-Defense Force (a vet who survived Outer Heaven); Big Boss works with the JSSDF as a combat trainer and analyst under the guise of a UN general.

2015, July: Shinji Ikari is summoned to Tokyo-3 to pilot Evangelion Unit One, just as Sachiel attacks Tokyo-3. **The Angel Wars** have begun.

* * *

Hidden Facility inside Mount Tarumae - Hokkaido, Japan

Present Day, A.D. 2015.

The massive mountain facility that was located underneath Mount Tarumae was originally designed to shelter Japanese civilians and its government in the case of nuclear war breaking out between the United States and the Soviet Union.

However, in the years following Second Impact, the facility has been given a new life...for a much darker purpose.

That purpose was to house the mass-produced Evangelions that Seele intended to use to unleash Third Impact once the Angels were destroyed. So far, nine of the massive behemoths were completed, each armed with a duplicate Lance of Longinus. Originally, there was supposed to be twelve mass-produced EVAs, but the facility had suffered some damage thanks to falling debris following the arrival of Sahaquiel some months earlier, destroying three of the half-built EVAs.

Seele had been hit pretty hard in the past couple of months. Two of their members – Seeles 02 and 05 – had been killed under mysterious circumstances, reducing the 12-member council to just ten. On top of that, the various locations in which the parts for the mass-produced EVAs were built had been wiped out in a series of tactical missile strikes all over the world.

And now, three members of Seele – two men and a woman – were there on a surprise inspection tour. The facility's head scientist, Dr. Itagaki, conducted the tour.

"We had some damage to the facility following the attack from the Tenth Angel," Itagaki reported as they stood on a walkway, watching the technicians and maintenance crews work on the massive weapons, passing guards armed with assault rifles. "I am sad to say that three of the EVAs will not be active when the time comes. Chairman Keel will have to settle for nine."

"Chairman Keel has already been notified of the incident," Seele 10 replied. "Are the EVAs designed to meet the Instrumentality Committee's standards?" he asked.

"Yes," Itagaki replied. "Each one is armed with a duplicate Lance of Longinus, as well as powered by a working S² Core, thus eliminating the need for internal batteries and power cords. They are also capable of flight, as you can see by the retractable wings on their backs. Of course, given the EVA's size and mass the wings are used in concert with AT Field-based levitation. Each EVA is controlled by a Dummy Plug, courtesy of Nerv. Unlike their Dummy System, we used Tabris' data, thus eliminating the human element from their actions."

"Speaking of Tabris, how is he?" Seele 11 – the only woman to ever sit on the council – asked.

"Tabris is at the moment, in the middle of a synch test," Itagaki replied. "I am heading there right now. Please follow me."

* * *

On the bridge which overlooked the entire facility, a video feed showed the inside of the Entry Plug. Its sole occupant was a pale-skinned teenage boy with white hair and red eyes, which were at the moment closed.

Born in the aftermath of the apocalyptic event known as Second Impact, Tabris - also known as Kaworu Nagisa - was reared by Seele, trained for this specific purpose. Upon his death at the hands of the EVAs under the control of Nerv, will Seele make their move against Nerv and its commander.

The Entry Plug was partially submerged in LCL, and was being monitored by technicians. Watching the synch test from the bridge, was Dr. Itagaki and the three Seele members.

"How is Tabris, Doctor Itagaki?" the man only known to the employees as Seele 11 asked.

"His synch tests are extraordinary," Itagaki replied. "His synch scores are at a stable 200.98 percent. Not even the three Children combined can touch his synch score."

The three Seele members exchanged glances. "I take it you haven't heard?" Seele 04 inquired. Off Itagaki's confused look, Seele 04 continued. "During the battle with Zeruel, the pilot of Unit One – the Third Child – has reached 400 percent, and was absorbed into the EVA's core. He remained there for 30 days before being released."

If anything, Itagaki was not impressed. "Am I to be worried? Those Children are nothing compared to Tabris."

"You really should not underestimate the power of the human spirit."

A image from inside the Entry Plug appeared on the monitor. Kaworu was listening in on the conversation. "We have guests, I see," he noted, looking at the three Seele members.

"You may come out, Tabris," Itagaki said. "The tests are now over."

* * *

Nine minutes later, Kaworu emerged onto the bridge, clean from the shower, dressed in a school uniform. Hands in his pockets, he was whistling 'Ode to Joy' as he approached Itagaki and the three Seele members.

"I take it you are from the old man?" Kaworu inquired.

Seele 04 nodded. "That we are," he replied. "Chairman Keel sends his regards, and wishes to see how you're doing."

"As you can see, Dr. Itagaki is taking care of me," Kaworu replied. "So tell me...who is this Third Child who managed to reach 400 percent and live to tell about it?"

Fortunately, Seele had files on all Nerv employees on file and it took Itagaki several seconds to punch in several keys on the console, causing the Third Child's profile to appear on a monitor.

Kaworu looked at the picture; a teenage Japanese boy with dark brown hair and cobalt eyes. From the look of things, he seemed ordinary.

"Shinji Ikari," Itagaki read. "Born 6 June 2001. Parents are Dr. Yui Ikari, who worked on Project E at Gehirn as a bioengineer, and Gendou Rokubungi, the current Commander of Nerv. Was sent to live with a teacher for ten years following an accident in which Dr. Ikari's soul was absorbed into Unit One during a contact experiment. Grandfather is Ryuji Ikari, also of Seele, who had unfortunately passed away following the failed experiment with Unit One. Was summoned to Tokyo-3 by his father to pilot Unit One against the Angels. So far, he has six solo kills to his name."

Kaworu studied the profile for a moment. "Shinji Ikari, huh? Sounds like an interesting person."

"Remember your mission, Tabris," Seele 11 warned. "You are to go to Tokyo-3 once the Sixteenth Angel is destroyed."

"No need to worry," the Angel of Choice replied. "I know my duty."

Before another word could be said, the entire facility shook violently. As if something big was trying to break into the hangar.

"What was that?" Seele 11 demanded.

"That was not us," Kaworu said.

That was when all Hell had broke loose.

**KA-BOOM!**

The massive blast doors – big enough for the mass-produced EVAs to step through, were literally blown open, the mangled metal doors flipping like giant shurikens, crushing several workers underneath.

Then they came stomping in, through the smoke and flames.

There were three of them, just as tall as the EVAs, amphibious in appearance.

Kaworu was facing the next-generation Metal Gear RAYs.

The armed guards began to open fire with their machine guns...and were brutally decimated by the leading RAY's return fire, riddling technician, scientist and guard alike with 20-millimeter rounds, fired from their flipper-like arms. The other two RAYs turned their attention to the nine EVAs. Launch silos opened on the RAYs' backs and on their knees, and the two Metal Gears launched their payload of missiles at the EVAs, demolishing them and catching numerous workers in the blast.

Back on the bridge, Itagaki turned to one of the technicians. "Get on the horn! We need help!"

"I can't reach anyone!" the tech replied. "The communication lines are down!"

Seele 11 then turned to Kaworu. "Tabris! Do something!"

As the RAYs launched their payload, Kaworu quickly responded.

One of the mass-produced EVAs sprang to life and activated its AT-field, shielding it from the destructive force of the missiles, which had all but destroyed the remaining EVAs where they stood, as they had not been outfitted with the Dummy System.

Gripping a duplicate Lance of Longinus, the remaining EVA turned to face the trio of RAYs.

The first RAY's mandible opened up, preparing to fire its primary weapon.

The EVA charged, preparing to impale the lead EVA.

Then the lead RAY fired.

Unlike the first-generation RAY, which used a water cutter for its primary weapon, the second-generation RAYs used the ultimate in advanced anti-EVA (most importantly, anti-AT field) technology.

The powerful ion beam penetrated the AT-barrier, striking the EVA in its S²-powered core, obliterating it, and sending it flying back, where it landed in front of the bridge in a heap.

Then the lead RAY took aim and fired off its own payload of missiles at the bridge. Kaworu was able to get his own AT-field up, but the blast rendered him unconscious, while Itagaki, the three Seele members, and the technicians were killed.

* * *

Kaworu slowly came to, and found himself the sole survivor of the destruction that had surrounded him. Grunting in pain from the shrapnel that had pierced his side, Kaworu shakily made it to his feet, holding his injury in order to stop the bleeding.

The mortally wounded Angel hybrid looked out at the shattered windows overlooking the hangar, and saw the extent of the damage. Bodies laid strewn all over the place, some crushed under debris. The nine mass-produced Evas were all destroyed.

A loud roar came from the hangar area, as Kaworu discovered that whatever had attacked the facility, was still there.

The massive, amphibious-like mecha which had single-handedly destroyed the facility rose from its hiding place. For one long moment, the Angel and the machine looked at each other, as if daring the other to make a move.

* * *

A few miles away, a lone figure watched the image of Kaworu being transferred to him onto a PDA. Within seconds, the computer had identified Kaworu.

**TARGET: KAWORU NAGISA – CODENAMED TABRIS, ANGEL OF CHOICE.**

**TERMINATE? Y/N?**

One gloved finger punched in **Y**.

* * *

Back inside the destroyed facility, the massive Metal Gear rose several more feet, so that Kaworu was looking at its chest area...

...which had popped open, revealing its deadly cargo.

Kaworu's eyes widened as he recognized the weapon within the Gear.

An N² Mine.

The RAY dropped the mine on the floor before making its retreat.

Kaworu simply closed his eyes and waited for the end. He didn't had to wait very long.

* * *

The Japanese night lit up with the power of a thousand suns as the force of the N² Mine had all but obliterated the hidden facility, as well as the final Angel in a deadly, concentrated blast.

The old man watched from a safe distance, the wind rustling his long white hair and trenchcoat, revealing the dual bandoleers – one slung over his shoulder, while the other was around his waist, each holster containing a Colt Single Action Army revolver. In any case, the man looked like (and was in fact) a gunslinger.

Revolver Ocelot turned from the spectacle, a smug grin on his wizened old face. The next-generation Metal Gear RAYs had done as it was advertised. Now it was time to leave the scene. His car was nearby, so it was just a short walk back to the vehicle.

'That will put a nice wrench into Seele's plans,' Ocelot thought as he entered the passenger side.

Behind the wheel, was Ryouji Kaji.

"So...is it done, Shalashaka?" Kaji asked.

Ocelot nodded. "The mass-produced EVAs are destroyed," he reported. "As well as Tabris."

"This will set Seele back indefinitely," Kaji said. "Knowing Keel, he will most probably focus on finding out who attacked the facility and killed Tabris. Those mass-produced EVAs were the key to unleashing Third Impact. He will not take this very lightly."

"And now, that key is gone," Ocelot said as Kaji drove away from the scene. "Your orders are to remain in Tokyo-3 for the time being. Keep an eye on things from within Nerv, as well as look after the boy. These orders come from the man himself."

Kaji nodded as he put the car into gear and sped away. "Understood."

As Ocelot and Kaji departed from the scene, rescue workers and several helicopters had arrived on the scene. But even they could see that it was no use. Whoever was inside or within the mountain facility was gone, as the N² Mine had triggered a massive eruption that would make the front page of the Shibun the following morning.

* * *

Location – unknown, the following day.

Once the news of the attack of the Tarumae Facility became known, the mysterious, Illuminati-like organization known as Seele was in a complete uproar. Decades of work, decades of planning to achieve Instrumentality was all but gone. Out of the twelve monoliths, only seven are present.

Finally, the monolith labeled **SEELE 01 – SOUND ONLY** called for silence. The remaining monoliths immediately obeyed. "Do we have any idea as to who was responsible for the attack on the Tarumae facility?" Keel asked.

A video image popped up, showing the attack on the hidden facility.

"We managed to get this video feed from the facility before it was destroyed in the N² blast," Seele 03 reported. "Whoever it was, they knew where and how to strike."

"What the hell is it?" Seele 07 asked, as the picture froze on the image of the RAY. "It it an EVA?"

"No," Seele 06 replied. "It's definitely not an EVA. Its weapons system is far more advanced."

"First, we lose both 02 and 05 to unknown circumstances," Keel began, "followed by various attacks on our facilities...and now, this...not only we lose three more of our members, but we lost the mass-produced EVAs and Tabris. There is more to it."

"Could it be Ikari?" Seele 09 asked. "Could he be capable of this?"

"Ikari is capable of many things, given what has at stake," Keel replied, "but not even he is capable of this. Nor did he know about the hidden facility. Someone else is responsible for this. Someone who wants to stop us from achieving Instrumentality."

"Our plans for Human Instrumentality were riding on the mass-produced EVAs to force Unit One to trigger Third Impact!" Seele 03 shouted. "All our planning was for nothing!"

"We can still use the forbidden union of ADAM and Lilith," Keel said. "But for now, I want an investigation into who was responsible for the attack in Tarumae. Instrumentality can wait for the moment. We must find these interlopers and eliminate them." The old man paused briefly. "Whoever this entity is...Number 03 is right. They know who we are, and where to attack with brutal precision. As for Ikari, we will watch him closely for the time being. Understood?"

Once the monoliths answered in the affirmative, they blinked out, Keel's monolith was the last to blink out of existence.


	2. Episode 1: Clash of the Pilots!

_**Episode 1: Clash of the Pilots! Ikari versus Sohryuu!**_

Snafu's Notes: I had the first two chapters written out already. And since most of the reviews were positive, here's Episode 1.

The Geofront, underneath Tokyo-3.

A synch test was in progress.

Nerv's three top pilots were inside their Entry Plugs, eyes closed, concentrating. Their images were beamed back to the command bridge, where they were being monitored by the Project E chairwoman and the Tactical Operations Director. Also present was the Nerv Commander, Gendou Rokubungi Ikari, and his Deputy Commander, Kouzou Fuyutsuki; Gendou seated in his chair, back hunched over, hands steepled together, hiding his face, the amber-lensed sunglasses hiding his eyes, while Fuyutsuki stood behind and to Gendou's left.

Also present was the recent addition to Nerv. She was a foreigner, most definitely, and made plenty of male (and some female) heads turn when she stepped into the room, not to mention making both Ritsuko and Misato jealous. The woman served as a second physician to the three Children, as well as the resident psychologist. She had arrived in Tokyo-3 the following day after Zeruel's assault on the Geofront, highly recommended by Nerv-01 in America. The woman was in her early thirties, with dark brown hair tied into a ponytail, dark brown eyes that screamed intelligence, and exotic to match. Like the Project E chairwoman, she had on a lab coat over her attire - a dark green blouse and a black skirt.

The black Nerv ID with its distinctive logo – an upside-down apple with half of the maple leaf superimposed over it – identified her as **Dr. Naomi Hunter**.

Meanwhile, the three bridge bunnies who were monitoring the synch ratios, were chatting amongst themselves.

"Have you heard about the eruption up in Hokkaido a couple of days ago?" Lieutenant Shigeru Aoba asked the bespectacled male bridge bunny.

Lieutenant Makoto Hyuuga nodded. "Yup. The MAGI recorded it. Tarumae finally blew its top. Good thing that the surrounding area was deserted," he replied. "It was only a matter of time, I guess."

"So what do you think about the new girl?" Aoba asked.

"Doctor Hunter? She is definitely hot. So what do you think, Aoba? Is she hotter than the Major?"

"That's a tough question," Aoba shot back. "Doctor Hunter could give Akagi and Katsuragi a run for her money. And the fact that she is a gaijin make her even more hot."

"I even saw the Commander and the Deputy Commander stare at her as she walked past them," Hyuuga said. "She's already shot down most of the men's offers for a date. So where do you think she's from?"

"Dunno. But rumor has it that she's not American by birth. I heard that she was originally British."

"The techs said that as well," Hyuuga said, adjusting his glasses. "I'm thinking she's Ivy League."

At that moment, Lieutenant Maya Ibuki's image appeared on the men's consoles. "Keep it down, the both of you," she snapped before her image blinked out.

Hyuuga and Aoba ignored her. Returning to their consoles, they continued to monitor the three Pilots' synch ratios. "Ikari's synch ratio has climbed ever since the last Angel attack," Hyuuga noted.

Aoba nodded. "That's not the only thing that's changed about him," he said.

"Can you really blame him?" Hyuuga replied. "He was forced to pilot without any training by his father, and we stood by and did nothing as Unit One tore apart Unit Three."

Maya's face appeared once again in the lower left corner of Aoba and Hyuuga's screens. "Shut up, both of you," she hissed. "If we haven't used the Dummy Plug, then...then.."

"Then what?" Hyuuga hissed, thankful that Commander Ikari could not pick up their feed. "Maya, we watched as Ikari's Unit One tore apart Unit Three, with his best friend inside. Suzuhara is crippled for life. We had the power to stop it, but we didn't, for fear of the Commander. Shinji pleaded with his father, begged him to stop. But he didn't. Killing Angels is one thing, but having damn near killed an innocent human being on the threat of death is another. We all deserve Shinji's contempt."

It was true. In the two months following Zeruel's attack on the Geofront, the estranged son of Gendou Ikari had become less withdrawn. He had became colder towards not only the bridge bunnies, but to his fellow pilots, Doctor Akagi and Major Katsuragi. Since Commander Ikari did not see Shinji as his son, Shinji gave him the same courtesy, viewing his estranged father with nothing but hatred and contempt, even publicly disowning the older man as his father on the bridge.

To add insult to injury, he addressed Gendou by either his first name or his maiden name, which irked the elder Ikari to no end, forcing him to have Fuyutsuki deal with his offspring. Commander Ikari could have reprimanded his son, but Shinji held a slight edge over his father. He was the only one who could pilot Unit One, since the EVA had rejected the Dummy Plug.

The only people he talked to aside from Doctor Hunter were Deputy Commander Fuyutsuki, and Asuka's former guardian, Ryouji Kaji.

Aoba had to agree with his male counterpart. "If anything, Pilot Ikari is more dangerous than his father," he said. "He's the one piloting Unit One. If it wasn't for the good doctor, he would have probably killed us a long time ago, and probably all of Tokyo-3."

That was also true. Naomi was by far, along with Fuyutsuki and Kaji, the only people who could actually speak to Shinji without the young pilot telling them in no delicate terms to fuck off.

The rest of the synch test went on in silence.

* * *

After another hour of testing, the synch tests were complete. Within minutes, two of the three Pilots had entered the command bridge. The other Pilot simply exited his Entry Plug and headed for the showers, completely ignoring the other two pilots as if they were not worth the time.

Asuka Langley Sohryuu strode towards Ritsuko, Misato and Doctor Hunter with her usual gusto, while Rei Ayanami remained behind, as she was speaking with Commander Ikari. The half-German ignored the newcomer and spoke directly to the chairwoman of Project E.

"So how did I do?" the half-German asked, direct and to the point.

Doctor Ritsuko Akagi scanned the sheet of paper she had in her hand. "Your synch score is at 70.11 percent, while Ayanami's synch score is at 60.97 percent," she reported. "Your score has dropped down somewhat, but you're still in the range."

"And what of the baka?" she asked. "He scored lower than me, didn't he? Ha! I knew it! Baka-Shinji is dead last!"

Before Ritsuko could say anything, Naomi spoke, cutting Asuka off in mid-gloat. "Actually, Pilot Ikari's synch score stands at 97.89," she stated, her proper Ivy League accent evident in her Japanese. "Lieutenant Ibuki ran the numbers twice."

"WHAT?" Asuka screeched as she yanked the paper from Ritsuko. Sure enough, Asuka saw that not only was she second, but that Shinji was ahead of her by nearly 30 points. By this time, both Ikari and Fuyutsuki had heard Shinji's synch numbers and were listening in.

Asuka was furious. "That baka has a higher synch score than me? The great Asuka Langley Sohryuu? He is nothing compared to me! I am the best EVA pilot!"

"You claim to be the best, yet you have only two solo kills to your name, whereas Pilot Ikari has seven," Naomi pointed out. "I'm simply stating the facts, Pilot Sohryuu. For all of your training and years of preparation, your boasting, and your intelligence...you're second best."

"How dare you!" Asuka shouted.

"Don't like it? That's too bad," Naomi continued. "If you claim to be the best, you have to prove it. From what I've seen of you, you're just a poser with an inferiority complex. Your recklessness and ego will endanger all of humankind. You're not the best, Sohryuu. You're just a liability. Plain and simple."

By now, Commander Ikari, Rei, Deputy Commander Fuyutsuki, as well as the bridge bunnies, Misato, and Ritsuko watched as Naomi matched wits with Asuka. The redhead was fuming, while Naomi remained looking rather smug.

"You...you..." Asuka sputtered.

"Choose your next words carefully, Pilot Sohryuu. Remember that it's my recommendation that is between your piloting EVA and a one-way ticket back to Germany," Naomi replied, her smile as fake as it was sweet.

That shot Asuka down. Slowly, the threat of being sent back to Germany became real with that single sentence. Naomi was pretty high up on the hierarchy, her authority rivaling that of Ritsuko and Misato's own, which meant that she could easily back up her saw that she had won. She knew the Plots' weak points and could exploit them to her advantage.

"I see that got your attention. How would those in Nerv Germany would take it if you were stripped of your duties of defending the world once they find out that you're a liability?" Naomi continued. "More importantly, how would your father take it to see that his daughter was nothing more than a failure?"

Asuka's hands balled into fists. She wanted to punch this woman out so bad, but somehow, she held her temper in check.

Deciding that she had embarrassed the hotheaded German enough, Naomi brushed her off. "Get to the showers, Pilot Sohryuu. That LCL smells like blood. Oh, and watch how you speak to your betters from here on out, or else you will be on the next flight to Berlin...without your precious Unit Two."

Asuka growled as she turned on her heel and stalked out of the command bridge, muttering choice curse words in German. She could not lift a finger to Dr. Hunter, but Shinji was fair game.

And to Asuka, the baka had a lot to answer for.

* * *

Stepping out of the locker room, dressed in his school uniform, knapsack over one shoulder, earbuds in his ears, his SDAT playing Mozart's 'Dies Irae,' the Third Child, one Shinji Ikari was looking forward to a nice night at home, following this round of synch tests.

He didn't bother to stay around to hear the results of the synch test. He was certain that either Naomi or Fuyutsuki would page him the results on his cellphone. All he wanted to do was to get home and relax.

His cellphone vibrating in his pocket had interrupted his chain of thought regarding his plans. Shinji retrieved the item from his pocket and flipped it open. It was a text message from Naomi.

_**Shinji. Synch score was 97.89 – nearly 30 points higher than Sohryuu. Red Devil is on the warpath, looking for you. Watch your back. Naomi.**_

Shinji smiled briefly before flipping the phone closed. Unlike his former father and most of the Nerv senior staff, Naomi - along with Fuyutsuki and Kaji - did nothing wrong by him. He knew that this was coming. Asuka was totally predictable. He placed the phone inside his backpack, along with his SDAT. He wasn't going to run away this time. After showing the deadbeat, his faux-blonde mistress and the rest of the Nerv bridge staff that he wasn't the same Shinji Ikari anymore, he saved Asuka for last.

And oh, was this going to be the proverbial coup de grâce.

A somewhat sinister smile spread across his lips as he remembered a line from a pre-Second Impact film. 'If revenge is a dish best served cold, then put on your Sunday finest. It's time to feast.'

Sure enough, Asuka came storming around the corner, still in her plugsuit, reeking of LCL. To her, her shower could wait. She had a bone to pick with the pilot of Unit One.

Hey! Third Child!"

Shinji turned around. "What now, Sohryuu?" he asked, obviously not amused.

"How in the hell did you beat my synch score?" the hotheaded German demanded, poking into his chest with one finger. "I'm the best Pilot! You're nothing compared to me, you little worm! You better start scoring lower than me, or else!"

Shinji swatted Asuka's hand away. He just about had it with this annoying bitch. By this time, Commander Ikari, Deputy Commander Fuyutsuki, Doctors Hunter and Akagi, Major Katsuragi and Rei Ayanami had caught up with the two pilots.

Normally, Shinji would be kowtowing towards Asuka, solely to avoid confrontation. Not this time. Not anymore.

"Or else what?"

Asuka blinked. Shinji never talked back to her. In fact, he never stood up to her.

"The only thing you are good at is whining," Shinji said. He then mocked Asuka. "'I'm the best Pilot. I'm the great Asuka Langley Sohryuu.'" He scoffed. "Please. You're just a goddamned joke. Everyone here knows it, Sohryuu. You know it. You don't like it? Tough break."

As Shinji turned to walk away, Asuka grabbed him by the shoulders and forcibly spun him around.

"Don't you dare turn your back on me, you spineless baka!" Asuka snarled as she grabbed Shinji and spun him around, a handful of Shinji's shirt in one hand. "You can't hide behind that restraining order while you're here! I swear to God that if you don't start lowering your synch score, you're gonna regret it!"

Shinji's reply was unexpected, even for Asuka. "No," he replied.

Then he followed up his reply by smashing his head into Asuka's nose, the force of the headbutt causing Asuka to let Shinji go as she stumbled back, holding her nose, eyes wide open in disbelief as to what had happened.

Shinji Ikari, in her mind, the Universe's bitch, has just struck her. Hard.

The gathered audience had different degrees of shock and disbelief on their faces. Even the normally aloof Commander Ikari and the impassive Rei Ayanami were shocked to see Shinji defend himself.

As Asuka Sohryuu would soon find out, she had bitten off more than she could chew.

As everyone watched, Shinji assumed a fighting stance. His right was held closer to his face, the hand not clenched into a fist, but rather open, palm facing downward, which could attack or defend at a moment's notice, while his left arm was extended, bending slightly at the elbow, the hand also open, knees bent slightly (think the stance K' uses in King of Fighters).

Naomi's eyes narrowed slightly in recognition of the stance. It was a basic close-quarters-combat stance, and only three people used that stance. One was dead, another was in America, while the other was here in Japan working with the Japanese Strategic Self-Defense Force.

At least, that was the cover story.

"You..you..." Asuka sputtered, revealing her bloodied nose. "YOU BASTARD!"

Asuka charged, cocking her left fist back. Shinji held his ground, as Asuka let the fist fly...

..only to see Shinji sidestep the punch.

Naomi knew what was coming up next. Close-quarters-combat drew on elements from various grappling and hand-to-hand style, like Jujitsu, Judo, Akido, and Krav Maga.

Shinji's hand snapped up and caught Asuka's outstretched wrist. Asuka felt the breath rush out of her body following Shinji driving his knee into her torso. Then he flipped her to the ground. The German redhead landed on her side hard, causing everyone watching (Commander Ikari included) to wince from the impact.

Asuka, on the other hand, was steaming. This definitely was not supposed to happen. She got back to a vertical base, as Shinji got back to his stance.

'Know your enemy, and know yourself. One thousand battles, one thousand victories,' Shinji thought as he patiently waited for Asuka's next move.

Asuka rushed in, throwing several punches, all which Shinji blocked and parried. Asuka felt the breath rush out her body as Shinji rammed his fist into her gut, which was followed by a left cross across her face. He completed the combo with a boot-to-da-head.

Asuka went down again.

"Is this what the German military has been teaching you?" Shinji taunted as Asuka spat out a wad of blood. "Poor performance, indeed. I wonder if you use your college degree and military training to wipe your ass, Sohryuu. 'Cause it's not working for you."

Shaking the stars out of her vision, Asuka got back to her feet. It became clear to everyone watching that Asuka was pretty much outclassed. The last thing anyone would guess was that Shinji Ikari facing down Asuka Sohryuu without breaking a sweat.

To add insult to injury, Shinji began to slap Asuka around, listing off the major offenses she had done to him as she attacked him yet again.

**SMACK!**

"That's for hitting me on the super carrier when we first met!"

**SMACK!**

"That's for screwing up the first time against Israfel!"

**SMACK!**

"That's for being such a crappy kisser!"

**SMACK!**

"That's for kicking me in the head while crawling inside the air vents!"

**SMACK!**

"And that's for destroying my cello!"

**KA-POW!**

The final backhand sent Asuka spinning to the ground, her face covered in numerous bruises, Shinji drawing blood from Asuka's lip from the impact of the final blow. Asuka stumbled back to her feet shouting obscenities in German, cursing Shinji. This time, she went for a kick to the groin...

...only to miss when Shinji kicked low, striking Asuka in her upper leg, before kicking her in the side of her head, knocking her down once again. "You're pathetic, Asuka," Shinji deadpanned. "You only pilot to stoke your ego. You put on a big show, acting as if you're strong, when you're just a weak little girl. You're not even worth the dust beneath my feet. You...are...nothing."

By this time, Asuka was seeing red. In her mind, Shinji was going to pay. With a feral scream, she charged.

Shinji grabbed Asuka's wrist when she tried to punch her with his left hand, while his right clamped down on Asuka's throat. The Second Child's eyes bugged out of her head as Shinji increased pressure on her windpipe, She tried to break free, but to no avail. In the back of her mind, she wondered how in the hell did Shinji get so damn strong.

No one dared to stop Shinji. If he could do what he had done to Asuka, then given the fact that he clearly despises the majority of the senior Nerv hierarchy as a result of what had happened with Bardiel and the Dummy Plug, no one dared to stop him. Not even Section 2, who had watched as Shinji take apart Asuka with brutal precision.

Not to say that Commander Ikari had tried. Gendou tried to stop Shinji from strangling Asuka to death. "Third Child, release the Second Child at - "

Shinji's head snapped around to stare at the Nerv Supreme Commander, the elder Ikari's voice caught in his throat at the glare from his son froze him in mid-speech. Gendou was well-known for his own cold glare, but his son's own glare was giving even Gendou a serious run for his money, Shinji's withering, emotionless gaze was more than enough to silence even the indomitable Gendou Ikari into submission. Even Misato and Ritsuko were frozen in place. Rei looked petrified.

The eyes were starting to roll back into Asuka's head as the lack of oxygen was starting to get to her as her attempts to break free grew weaker.

"Shinji."

Shinji's gaze turned onto Naomi. Unlike most of Nerv, only Naomi Hunter was immune to Shinji's ice-cold glare. After all, she had been intimidated by better.

Naomi placed one hand on Shinji's shoulder. "Please let Pilot Sohryuu go," she said calmly, looking Shinji full in the eyes. "You have done enough."

At Naomi's request, Shinji finally relented. He released Asuka, who fell to the ground, coughing, taking in deep gulps of air.

As Ritsuko and Misato rushed in to check up on Asuka, Shinji had picked up his backpack and slung it over his shoulder. Turning to Gendou, he said in a cold voice, "Next time she attacks me, I'll put the red bitch down."

That said, Shinji Ikari left Central Dogma. No one dared to stop him. Not even Section 2. Not after witnessing how he had taken apart Asuka Sohryuu without breaking a sweat.

Things had definitely changed around Nerv since the last Angel attack. Shinji Ikari himself was one of them. And the senior Nerv hierarchy knew that they were responsible for Shinji's change in attitude towards them.

Misato and Ritsuko accompanied Asuka to the infirmary, while Gendou and Fuyutsuki headed for his office. Gendou knew that he could not discipline his son. Not for self-defense. So he decided to drop the matter. Rei headed for the showers, visibly disturbed by what she had seen.

Only Naomi was left. Once she was inside her office, the door locked, she retrieved her PDA and dialed a number. Within seconds, someone answered.

"Yes?"

"It's Naomi, sir," Naomi spoke into the PDA, switching from Japanese to English.

"Ah, little Naomi," her benefactor said. "To what I owe the pleasure of this call?"

"I noticed that you have taken on a student in CQC. He's a bit rough, but he shows promise."

"You mean the Ikari boy. Yes. The kid is a natural when it comes to CQC," her benefactor admitted. "He reminds me of your brother."

Naomi stiffened slightly at that. Even now, her adopted elder brother was still a sore subject for the Rhodesian beauty. After the truth concerning her parents was revealed to her. Part of her hated Frank for killing her parents, but another part of her still loves him.

"Anything I need to know about Nerv?"

"Commander Ikari and Deputy Commander Fuyutsuki doesn't know about the destruction of the Seele facility, nor the death of the final Angel," Naomi reported. "If they do, then they are doing a good job of hiding it."

"Very well. Keep me informed."

"Yes, sir," Naomi replied, cutting the call. 'Things have become interesting,' the female doctor/Patriots mole thought. 'Interesting indeed.'


	3. Episode 2: The Legendary Soldier

_**Episode 2: The Legendary Soldier**_

One month earlier, following Shinji's return from Unit One's core...

Inside a secluded section of the city's park, Shinji Ikari sat on a bench, alone. To say that he was depressed was a total understatement.

Given the fact that he currently had Misato's service pistol in his hands, having pilfered it earlier from her belongings earlier that day, it was clear that he was suicidal.

It had started following Zeruel's attack on the Geofront. Never mind the fact that he had just saved everyone from Third Impact for the seventh time. He was still treated like dirt by Asuka (who had destroyed his cello earlier that day, saying that she was bored) and snubbed by Ritsuko. Even more worse, Touji and his family blamed him for what had happened with Zeruel. Not that Shinji could do anything about that, since it was his bastard of a father that had used the Dummy Plug and had nearly killed Touji. Even worse, Asuka had told everyone in class that it was Shinji's Unit One that had crippled Touji, effectively turning everyone against Shinji, while painting herself as the valiant heroine. Even Kensuke had turned his back on him.

But what hurt the most was Rei's reaction, following his return from the EVA's core, despite the fact that he had saved her life.

She had said only one word to him, after she had slapped him.

Coward.

Which is what led Shinji to where he was at now. Earlier that morning he had snuck into Misato's bedroom and had stolen her pistol while she slept in an alcohol-induced stupor. It was loaded, as it had always been. He made it through school, ignoring Asuka's heckling and the whispers and insults of the other classmates, all the while Misato's pistol was in his backpack, within distance. He wondered how many he could kill before turning the gun on himself.

He came close to revealing the pistol and putting a slug in Asuka's head, as well as Rei's. But he relented. Once school let out, he did not go back home. There were no synch tests to be done, so Shinji decided to head for the park.

Looking down at the pistol, he slid the slide back, making sure that a round was jacked into the chamber before snapping the slide shut.

'One bullet,' he thought. 'One bullet is all I need. It will be over. All over.'

Shinji flipped the safety off. After a moment, he closed his eyes and raised the gun to his head.

Or at least he tried to, since someone had clamped down on the gun's barrel with one gloved hand. Shinji opened his eyes and looked at the person that had stopped him from taking his life.

It was a man – American by the look of things. He was also very old, older than Fuyutsuki. Shinji guessed that he was in his eighties, but in excellent shape. His hair was white, combed back neatly, the beard also white and neatly trimmed. His one good eye looked down at the distraught Ikari, while the other one – his right eye – was concealed by an eyepatch. The man was dressed in a officer's uniform, similar to what the Japanese Strategic Self-Defense Force would wear save that the jacket, tie and pants were black, and the shirt white. His posture radiated authority. Shinji saw that his rank was that of a General – four stars.

The man gently removed the pistol from Shinji's hand. He ejected the clip and pulled the slide back, the bullet flying from the open chamber.

"No need for you to go just yet, son." The man's voice was grizzled, but calm. His Japanese was perfect.

"Why...?" Shinji whispered softly. "Why did you stop me?"

The man countered with a question of his own. "Why are you trying to kill yourself?"

"I...I..." Shinji began before finally breaking down in tears.

* * *

About 20 minutes later...

A teahouse near the park.

Inside one of the booths, Shinji sat facing the man, who was sipping at his tea, acting as if he had not stopped him from committing suicide.

"Feel like talking, kid?" the old man asked. "You must have some serious problems if you had plan on putting a bullet in your head."

"You don't know the half of it," Shinji replied darkly.

"You got a name?"

Shinji gulped slightly. "Shinji. Shinji Ikari."

The old man nodded. "Name's John. So tell me about yourself, son."

It was as if the floodgates had opened up. Shinji told the old man everything. From being abandoned as a child following his mother's 'death,' to being forced to pilot the Evangelion in defense of the city, up to the point where John had found him.

John listened on with great interest. He waited until Shinji was finished. "So you're one of the three pilots of the huge mecha that has been defending the city?"

Shinji nodded.

"A noble accomplishment," John said. "But piloting the EVA is something that you don't want to do, correct?"

Again, Shinji nodded.

"Life is never fair, Ikari," John said sagely. "Trust me. As a soldier myself, I know first-hand."

Shinji looked up. "You're a soldier?"

"Soldier, mercenary, commander, operative," John rattled on. "Oh I've been many things in my life. You can say that I'm a legend of sorts within the defense community. And I sympathize with you in your plight. You fight for other people, yet they don't appreciate your efforts. They simply see you as a means to an end."

John's mind flashed back to a key event some fifty years ago. Even after all this time, it still made him angry.

Angry at how the American government he had fought for had slandered his mentor, portraying her as a war criminal to save their own asses.

Angry at how he was the one to end her life. At least he was able to exonerate her in the end.

"So why do you pilot the EVA?" John asked.

"Because if I don't then everyone will die," Shinji explained.

"You place yourself before others," the old man surmised. "Very noble of you, Ikari. That is a rarity in this day and age. Even before Second Impact, there are those who look out for themselves."

"You have any kids?"

'Not that I would call them my kids,' John thought darkly, thinking of the unusual circumstances of their birth. But he decided to answer truthfully. "A son. I had three, but two of them died shortly after the Impact. As for the other one, we were estranged at first...but we're on speaking terms. He's in America at the moment. I've been in Japan since the Impact."

John studied the boy closely. He recognized the effects of post-traumatic stress disorder in a heartbeat. 'And they continue to use him as a pilot,' he thought. He had seen the effects that PTSD had on child soldiers, which was why EVA had taken an interest in them.

"Do you feel better now?" John asked.

Shinji slowly nodded. "A little."

John nodded. "That is good to hear, young Ikari." He looked at his watch. "It's getting late. You should head on home. Your guardian may be worried."

Shinji shook his head. "She works nights, so I got the place to myself. Better for me, anyway, since I really can't stand Asuka." He slumped back into his seat. "I planned on shooting her at school today. I almost did it too. But I didn't."

'Yeah, the kid's definitely got PTSD,' John thought. 'Next time Naomi calls, I'll see that he gets treated.'

"I'm just tired," Shinji said, head bowed, shoulders slumped. "I'm tired of being afraid. I'm tired of running away from my problems. Tired of being used as a scapegoat. I want to be strong."

"Strength without determination means nothing," John rebuked calmly. "Determination without strength is just as useless."

For a moment, Shinji reminded the old veteran of a young half-Vietnamese kid. That same kid that would grow up into one of the finest operatives to ever carry the codename of Fox under his tutelage.

John saw quite a bit of Frank Jaeger in Shinji.

He then made a decision. One that he had hoped would at least help Shinji in the long run. "There is a saying, young Ikari. 'When the student is ready, the teacher will appear.' Are you serious in your wish? To become strong?"

Shinji nodded.

"There is a lodge near the outskirts of Tokyo-3. Follow the highway. You'll see it. On the days you don't have to train, be there. I will teach you how to stand up for yourself. How to move, how to think. Be warned, Shinji Ikari, I am not one to be taken lightly. You wish to train with me, then you must have focus and dedication. Understand?"

Shinji nodded. "Yes, Sensei."

"Another thing," John added. "Don't call me sensei."

Shinji was puzzled. "What do I call you then, instead of Sensei?"

John smiled. It sent chills up Shinji's spine. "You can call me Big Boss."

* * *

Two weeks had passed since that day. Since then, there had been a lull in the Angel attacks on Tokyo-3. Aside from the synch tests, Shinji was a frequent visitor at Big Boss' home.

Misato had questioned him about his whereabouts whenever he came home late, to which Shinji replied that he was just simply walking. Since Shinji didn't run away, Misato decided to drop it for the time being. He ignored Asuka, at home, at the Geofront and at school.

It also helped that sneaking in his SDAT was useful in drowning out the German girl's proclamations about how superior she was. Rei ignored him, which suited Shinji fine.

On the days he trained with Big Boss, the old man not only taught Shinji how to fight, but he also taught the boy valuable life lessons, using his own life as an example. As it turned out, Big Boss was not just a warrior, but he also took a philosophical approach in his life, something he had began doing shortly before Second Impact.

Shinji, on the other hand, became very interested in the old man's fighting style. Big Boss was a good as his word. But even Shinji surprised him. The boy was a fast learner, and given the amount of physical training he had to undergo at Nerv, he was pretty strong for his age.

To Shinji, he had found the father figure he was looking for in Big Boss.

* * *

Three weeks had passed since Zeruel's attack on the Geofront. And Shinji was once again a guest inside Big Boss' mountain lodge.

The old man had excused himself to take a phone call, leaving Shinji alone in the living room. The collection of photos that were on the mantle caught his attention. Standing up from his spot on the sofa, Shinji walked over to the mantle and inspected them. The pictures themselves told a story, of a life forged in the battlefield. Most of them were from his younger days, as the eyepatch was a dead giveaway. Also placed on the mantle, was a medal – the Distinguished Cross, pre-Second Impact.

Several photos stood out in particular. The first one was a group photo, formal, six people in total – four men and two women. As always, Big Boss was easy to pick out because of the eyepatch and the formal military uniform (i.e., the same one he wore in the ending of Snake Eater). He wasn't the only one in uniform. The older-looking gentleman with the scar on his face and the gray hair neatly combed back was also in uniform, Shinji recognizing it as that of the British SAS (Kensuke showed him a picture of the uniform before Bardiel). The two remaining men – the tall, African-American and the blond man were dressed in suits. The dark-haired woman had a conservative evening dress on, while the attractive-looking blonde woman on Big Boss' arm was dressed in a red Chinese cheongsam.

The small caption on the photo read **THE PATRIOTS – JULY 24, 1971**.

Photo number 2 was also of Big Boss, this time without the eyepatch, along with another woman. Like the other one, she was also a blonde, but she looked older than the younger Big Boss. A drab gray bandanna was wrapped around her head. Both were dressed in olive gray camo fatigues. Both were armed; Big Boss toting an AK-47, while the woman was armed with a strange-looking weapon. To Shinji, it looked like a modified carbine with a double drum mechanism.

Funny thing was how the drum was shaped like the symbol for infinity.

'Huh. Who's she?' Shinji wondered.

Photo number three was another group photo – over a hundred men in total. The photo had an older Big Boss in the center, looking sharp as always in his military uniform. Another older man, clad in the same uniform and beret stood next to him, the name tag reading **CAMPBELL**. One guy stood out for Shinji.

The guy was clean-shaven, gray bandanna wrapped around his hair but could pass as a mirror image of Big Boss in his younger days. Shinji remembered that Big Boss mentioned having a son, and suspected that this guy must be it.

The last photo that caught Shinji's eye was that of Big Boss and the attractive blonde. Both were in casual clothes, and apparently enjoying the other's company. It was also snowing in the picture.

Shinji did not even notice Big Boss walk up from behind him. "I see you're into my photos," he said, scaring Shinji. The old man chuckled. "Each one tells a story. As I've said, I've gotten around in my youth. Traveled all over the world."

"I see," Shinji said. He pointed to the photo of Big Boss and the older woman. "Who's she?"

Big Boss turned to the photo in question. "That's my mentor – a spiritual mother, if you will. She taught me everything I know. How to fight, how to fire a gun, how to stay alive. She never told me her real name. She was known as The Boss," the one-eyed commando explained, looking at the picture fondly. "Most people in the armed forces don't know about this but she is known as 'The Mother of the Special Forces.' Before I became her student, she was the leader of the Cobra Unit – a crack team of commandos who led the Allied forces to victory in the Second World War. She was also known as The Joy and my personal favorite, Voyedova - Russian for 'Warlord.'"

"So what happened to her?" Shinji asked.

Big Boss was silent for a moment. "She died...over fifty years ago. Died on her last mission."

Big Boss remembered her words to him shortly before their epic battle on the shores of Rokovoj Bereg.

_"One must die, and one must live. No victory, no defeat. The survivor will carry on the fight. It is our destiny. The one who survives will inherit the title of Boss. And the one who inherits the title of Boss will face an existence of endless battle."_

Even after five decades, The Boss' words ring true to Big Boss. He had been fighting for most of his life, even now, and he was growing tired.

"About the same time I got this," Big Boss continued, gesturing to the eyepatch, "she died, in service to her country and to her government. That was when I was awarded this," he said, pointing to the medal, "and my present title."

_"You are above even The Boss. I hereby award you the title of Big Boss."_

Shinji decided to change the subject. He pointed to the photo of the Patriots. "And this one?"

Big Boss picked it up and regarded it with a sad look on his face. "I don't know why I keep this photo. Maybe for sentimental value." He sighed. "We were all friends once." He pointed out the faces, identifying them by their names. "Zero, my former commanding officer. Dr. Clark, otherwise known as Para-Medic. Signt, his real name being Donald Anderson."

He tapped at the picture of the blond man. "Adamska, nicknamed Ocelot. He was a cocky little bastard, but I took him under my wing, like you, and trained him. Reckless at times but a good soldier." The last person was that of the blonde in the Chinese dress. "And that's EVA. We met around the same time that The Boss was killed. Loved motorcycles. Hell of a shot with a Mauser."

Big Boss's mind went back to that moment in the cave, in which EVA had consoled him following his first escape from Groznyj Grad.

"Snake...thank you. I'll be your eyes from now on..."

"You two were close," Shinji noted, pointing to the photo of the younger Big Boss and EVA.

The old man chuckled. "Can't put nothing by you, can't I, Ikari? Yes, we were together, on and off for many years." He stiffened slightly. "She died two years ago. I had her buried here in Japan. She always did love it here."

"So...what happened with those other guys?"

Big Boss was silent for a moment. "Back in those days, the United States and the Soviet Union were at each others' throats. East versus West – the Cold War. I was but one of the many players in that deadly game of tactical espionage action. After I was awarded the title of Big Boss, Zero came to me and pitched an idea. An organization dedicated to The Boss' ideas. The idea of a world united. Thus, the Patriots were formed." He gestured to the photo in his hand. "As you can see, I was also a member."

He placed the photo back on the mantle. "But..as the saying goes, 'power tends to corrupt, and absolute power corrupts absolutely.' Zero, Signt, and Para-Medic became drunk with power, thus corrupting The Boss' final wishes. They levitated my status as a soldier to the point that I was something of a messiah. I opposed them, along with EVA and Ocelot. Para-Medic was killed in a freak accident shortly after Second Impact. Zero was caught in the blast that leveled Old Tokyo. And Signt...well, he had heart problems. With EVA's death, Ocelot and myself are the remaining Patriots alive."

The old man regarded the photo for a moment, looking at Zero's image. "Even with so much bad blood between us...it's actually kind of funny. The hatred is gone. All I feel is a deep sense of longing. And pity. Even after all this time, I still wonder...did Zero really hate me? Or did he fear me? Either way, it's way too late to ask him now."

Big Boss then produced a worn book and handed it to Shinji. "Here. This should interest you. A true soldier does not rely on just brute force alone. War is always and will ever be based on deception."

Shinji looked at the title. The title read **The Art of War**.

"Are you familiar with Sun Tzu?" Big Boss asked. When Shinji shook his head, Big Boss continued. "He was a philosopher, a warrior and a general who lived in the era of warring states, back when China was still feuding kingdoms. The book you hold in your hands is his life's work. I applied his teachings to my daily life. You should do the same. There's a legend regarding Sun Tzu and the Emperor's concubines. Have you heard about it?"

Shinji shook his head.

"It was after he had completed writing The 'Art of War,'" Big Boss explained. "King Helu of Wu had read Sun Tzu's works and had challenged him to a test. Sun Tzu claimed that anyone could be trained as a soldier, so King Helu ordered him to train the one hundred and eighty concubines of the royal harem. Sun Tzu split them up two divisions, ninety women each, made the two senior concubines the division commanders and armed them with weapons. He showed them the maneuvers and ordered them to execute them when ordered. Instead, the concubines began to laugh. Sun Tzu turned to Helu and said, ' if words of command are not clear and distinct, if orders are not thoroughly understood, then the general is to blame.'

"When he ordered the concubines to perform the maneuvers again, they once again broke out in laughter. ' If words of command are not clear and distinct, if orders are not thoroughly understood, the general is to blame. But if his orders **are** clear, and the soldiers nevertheless disobey, then it is the fault of their officers,' Sun Tzu had said to Helu, right before decapitating the two concubines and appointing two more as the division commanders. Needless to say, the concubines performed the exercises flawlessly. Of course, Helu was upset that he had lost his concubines, but in the end, retained Sun Tzu as his general."

Shinji blanched slightly at the story.

"But it's a legend," Big Boss said, shrugging his shoulders. "No one knows that whether or not it's true. One of my favorite verses in that book is 'Be extremely subtle, even to the point of formlessness. Be extremely mysterious, even to the point of soundlessness. Thereby you can be the director of the opponent's fate.' That book will help you in how to live."

Shinji nodded. "Thank you, Big Boss."

The legendary soldier gave a small smile and patted Shinji on the head. "Now, it's time for you to return home. Start reading on that book."

Shinji nodded and placed the book inside his backpack.

* * *

Four weeks had passed since Zeruel's attack on the Geofront.

Gendou Ikari was mildly surprised to see Shinji strode into his office, thus interrupting his meeting with Ritsuko. "What is it, Third Child?" he asked, obviously annoyed. "I'm very busy."

Shinji stared down his father. In the past couple of weeks, even Gendou had taken notice of his son's change of attitude towards the other pilots and the senior Nerv employees, himself included. If Gendou Rokubungi Ikari was intimidating, then Shinji Ikari was like ice. It was as if he had stopped being meek and had simply closed everyone off, hiding his own emotions beneath a ice-cold mask that even sent chills down Gendou's spine...even if he didn't admit it.

Gendou also noted that Shinji was only civil to both his Deputy Commander and the Second Child's former guardian. In the back of his mind, he wondered that maybe using the Dummy Plug and knocking Shinji out by increasing the LCL pressure was a bad idea. If Shinji was starting to snap under the pressure, then his scenario – as well as his life, not to mention his subordinates – was in danger.

"I want a change in address," Shinji stated, plainly and coldly, his voice sending chills down Ritsuko's spine. "I want my own place."

Gendou responded with the same cold tone. "Your request is denied, Pilot. You will continue to reside with Major Katsuragi and Pilot Sohryuu, and that is your only option."

"Have it your way, _Commander_," Shinji replied, pronouncing Gendou's title with sarcasm as he retrieved his Nerv ID and tossed it onto Gendou's desk. Shinji was out the door just as the card slid to a stop in front of Gendou.

Gendou was unmoved. "Why am I not surprised? That boy always runs away. What a waste of time. We can still use the Dummy Plug for Unit One."

"That's the reason why I am here," the faux-blonde replied as she slipped a sheet of paper in front of the older man. "We have completed the tests on Unit One, and we got a problem. It appears that by using the Dummy Plug in Unit One, the core was weakened by 45 percent."

Gendou did not like where this was heading. "Meaning?"

"If we use the Dummy Plug one more time, then we risk losing the core," Ritsuko replied. "The MAGI just confirmed it three hours ago. There is no other way. Only Shinji can pilot Unit One."

Gendou digested the news with growing alarm. No core means no soul. No soul means that all his planning to get Yui back would be all in vain. Which meant that he needed his son to pilot.

He pressed a button on his desk, and spoke. "Find the Third Child and bring him to my office."

* * *

Shinji had made it to the lift that would take him to the city above when he met up with three of his father's Section 2 goons with orders to bring him back to Commander Ikari's office.

Within minutes, Shinji found himself standing before his father once again. This time, Ritsuko was not there, having returned to her labs not really wanting to deal with the younger Ikari. Gendou looked at his son for one long minute, trying to intimidate him as he always had done in the past. Only to find out that his withering glare was not working, as Shinji matched it with his own.

Gendou was out of options. In the back of his mind, he wondered whether or not his son would be a threat to his scenario. But for now, he would concede defeat.

"Third Child..." Gendou began, "if I agree to your demand for a residence transfer, will you remain employed with Nerv?"

"Yes," Shinji replied.

"Your request for a transfer is granted," Gendou conceded. "Anything else?"

"Two more requests," Shinji continued. "First, a transfer out of Class 2-A to another class, and a restraining order on Sohryuu. Outside of Nerv, she stays away from me."

Gendou contemplated these requests for a moment. Then he unlocked his hands and slid Shinji's ID towards his son. "Agreed. Your residence will be prepared by the end of the day."

Shinji retrieved his ID and exited the office.

Once Shinji was gone, Gendou sighed. Removing his glasses, his rubbed the bridge of his nose, feeling a migraine coming on. Up until twenty minutes ago, he was the undisputed commander of Nerv. Now, his own son had a ace up his sleeve. Should anything happen to Shinji, then he loses Yui.

Gendou placed his glasses back on and pressed another button on his desk. The image of Deputy Commander Fuyutsuki came up seconds later. "Professor."

"Sir?"

"Arrange a change in living quarters for the Third Child, effective immediately," Gendou ordered. "Second, arrange for his transfer out of his homeroom and into another classroom. Last, file a restraining order on the Second Child. She is to stay away from the Third Child at a distance no less than 500 feet. If she violates the order, then she will be stripped of her duties as an EVA pilot."

"Yes, Commander."

Fuyutsuki's image blinked out.

* * *

Katsuragi Asylum for the Drunk and Aggressive, later on that night.

Misato Katsuragi had seen the change in Shinji following the battle against Zeruel. And it worried her.

At first, Shinji grew more and more detached, and Asuka wasn't helping with her taunts and insults. Ritsuko even insulted him, despite the fact that it was Shinji that had saved their asses once again. Commander Ikari didn't give a damn, as usual. Add the fact that Asuka had stoked the fires at their school, effectively turning everyone against him in their classroom while painting herself as the heroine that had tried to rescue Touji, thus stoking her own oversized ego, Shinji was on the brink.

Then, it started several weeks ago.

The Shinji Ikari she knew was in layman's terms, a wuss. But now, Shinji had changed. It had started when Maya had tried to apologize to Shinji for using the Dummy Plug. The retort from Shinji could have stripped the paint job off of Unit One, and had sent Maya off running in tears. When Aoba and Hyuuga confronted Shinji about how he had treated Maya, they both were given the same treatment, the verbal barrage from the Third Child shocked even them.

Misato soon found out why. On Commander Ikari's orders, the Dummy Plug system was activated and his now-former best friend was nearly killed. Shinji had no love for his father, but this was the final straw. Whether it was either fear of his son piloting the massive bio-mecha or putting the Evangelion before Shinji, Gendou had knocked his son out by ordering the LCL's pressure increased.

Not even Misato herself was exempt. She was spared the verbal barrage, but Shinji's attitude towards the young Operations Director had all but cooled. But he did have several choice words for Ritsuko and his father. She knew that the Dummy Plug fiasco wasn't Shinji's fault, and Asuka's ego wasn't making things easier on him. Rei continued to ignore Shinji, who simply responded by giving her the cold shoulder. He refused to acknowledge the blue-haired girl's existence, which disturbed even the First Child.

Misato saw that Gendou's actions have all but destroyed his family. Not that he gave a damn. His main focus was getting Yui back at all costs. He never acknowledged Shinji as his son, to which Shinji responded in kind. He no longer saw Gendou Ikari as his father. In Shinji's words, he was nothing but 'a heartless bastard who breathed air,' and wondered what did his mother see in him, right before denouncing him in front of the Nerv bridge staff, saying that Gendou was 'a pathetic excuse for a father who does not deserve to have his mother's last name,' thus effectively forsaking him as his father. Gendou's response was 'irrelevant,' but even he was starting to grow concerned with Shinji's change in attitude.

Misato feared that Shinji was going to snap.

That was when Deputy Commander Fuyutsuki stepped in, offering to handle any and all matters in regards to the Third Child, thus defusing the tension between Shinji and Gendou, if for the time being. Fuyutsuki was away that day when Bardiel had struck, and thus, was spared Shinji's ire. He was also on good terms with her old flame, Ryouji Kaji. Even more so, he would come home late at night, and wouldn't say where he was at when asked.

Shinji had all but avoided talking to Misato. He even went as far as blocking her out during the synch tests, as well as Asuka. Since Misato still had problems in navigating around the facility, Shinji used that to his advantage, beating Misato out of the Geofront before she could corner him.

But not this time. Misato had finished her paperwork earlier than expected, meaning that Shinji would be at home by the time she would arrive. As she left the Geofront, she was stopped by Deputy Commander Fuyutsuki, who handed her a sealed envelope. Misato thanked the older man and made her way home.

Upon arriving at the apartment she shared with Shinji and Asuka, she received yet another shock.

A giddy Asuka Langley Sohryuu moving her stuff into Shinji's room. Shinji was nowhere to be seen. Pen-Pen had waddled back into his fridge, beer in flipper.

"Asuka, what's going on?" Misato demanded. "Where's Shinji?"

"Don't know, don't care," Asuka replied as she moved another box into her new room. "The spineless baka wasn't here when I came home, and his stuff was gone."

Misato groaned to herself. Shinji had ran away again. 'Wonderful. Commander Ikari's gonna have my head on a platter when he finds out about this,' she thought as she sat in her chair. 'Can't really blame him, though.'

Her cellphone began to ring. Upon looking at the ID, she saw that it was Kaji calling. She decided to ignore it. Right now, her main focus was to get Shinji back before Gendou found out that Shinji was missing.

Five minutes later, her cellphone rang again. It was Kaji. Again, Misato ignored the phone.

The third time her phone rang, Misato answered it. "What the hell do you want, Kaji?" she demanded. "Now is not a good time. Shinji's ran away again and I have no idea where he is."

"Actually, that's the reason why I'm calling," Kaji replied. His voice sounded serious.

Misato went rigid in her seat. "You know where Shinji is? Where is he?"

"He moved out," Kaji replied simply. "He moved to an apartment on the other side of Tokyo-3."

"How do you know?" Misato asked.

"I helped him move," was the reply. "And before you ask, I can't tell you where he is. He made me promise not to tell you. Can't really blame him for how he's feeling at the moment. He feels used, which is why he is acting so cold. He's also negotiated a transfer out of his homeroom, thanks to Asuka screwing him over by blaming the mess with Bardiel on him. Just give the kid some time to cool down. Give him some space. He already has enough on his shoulders with piloting EVA. Gotta go."

Kaji then ended the call. Misato slumped back in her chair, ignoring Asuka as she continued to move her belongings into the room once belonged to Shinji Ikari.

'I failed him,' Misato thought dejectedly. 'I failed as a guardian. I need a drink. I need several drinks.'

Misato rose from her chair and walked into the kitchen. After retrieving a six-pack of Yesibu, she trudged back to her chair. After draining two cans of beer, she noticed the envelope sticking out of her jacket pocket, and immediately remembered the aged Deputy Commander handing her an envelope before she had left for the night.

Misato retrieved the envelope and opened it. Pulling out a sheet of paper, she began to read. Her eyes widened at the realization as to what it was.

A notice regarding a restraining order.

**TO: PILOT ASUKA LANGLEY SOHRYUU - DESIGNATION: SECOND CHILD**

**FROM: NERV HIGH COMMAND**

**RE: RESTRAINING ORDER**

**Effective immediately, a restraining order has been placed against you by Pilot Shinji Ikari. Outside of the Geofront, you are to stay away from Pilot Ikari at a distance of no less then 500 feet. Failure to comply with this order will result in your duties as a EVA Pilot being revoked indefinitely. Continued harassment of Pilot Ikari will result in your immediate termination of employment with Nerv, along with you being sent back to Germany without your EVA.**

**Gendou Rokubungi Ikari, Nerv Supreme Commander.**

**Kouzou Fuyutsuki, Nerv Deputy Commander.**

* * *

Asuka would find Misato slumped over in her chair the next morning, along with a dozen empty beer cans littering the floor around her chair as she prepared for the day. It had appeared that Misato had cried herself to sleep, given the puffy cheeks and the tear tracks down her face.

'She's shedding tears over that baka?' Asuka thought. 'She'll see soon enough that we're better off without him. Gott, I'm hungry. That baka better have my lunch ready when I get to school, or else he's gonna wish he was stuck back inside the 12th Angel!'

It was then that the half-German noticed the sheet of paper in Misato's hand.

Shinji Ikari's apartment, at the same time.

The scream could be heard from miles. Inside a small apartment (similar to Rei's apartment, only cleaner and not run-down), Shinji Ikari smiled to himself as he ate his breakfast. Apparently, Asuka had just discovered the restraining order he had placed on her.

Today, he didn't have to be at the Geofront, so he would go and train with Big Boss. Also, today would be the day that he would be transferred out of Class 2-A and into another homeroom. So long as he was away from the Red Devil, he was more than happy.

**OMAKE!**

What if Shinji had decided to gun down Asuka and Rei?

Tokyo-3 Junior High School.

The teacher continued to drone on about Second Impact, putting most of the students to sleep. With the exception of Asuka, who was pestering Shinji by tossing paper balls at the back of his head, and sending him personal messages on the classroom's private message system, along with several other people - mainly Asuka's friends, Hikari included - telling him that he was nothing but a joke, and that he should just simply die.

Rei, as usual, ignored Shinji. She was looking out the window.

Shinji simply closed the PMs as fast as they appeared. He knew what they said.

"I don't like this trash can," Asuka snickered as she pelted Shinji with another paper ball, the teacher continuing to drone on about Second Impact.

Hikari snickered, not really wanting to step in to stop the abuse.

Had anyone been paying attention, they would have noticed the loaded H&K P8 pistol in his lap. But he had it so that no one could not notice. But due to the fact that most of the class was put to sleep by the teacher's lecture and the fact that Asuka sat several desks behind Shinji, they failed to see the inevitable time bomb that was about to go off.

It was when Asuka had tossed a pencil at the back of his skull that Shinji had finally lost it.

He opened up the PM message system and sent Asuka a message.

'Sorry, Asuka. Don't take this personal.'

Sure enough, as he flipped off the safety and gripped the gun in his hand, Asuka reacted in predictable fashion.

"What the hell are you talking about, you spineless baka? I got nothing to forgive you for..."

Those were her last words, as Shinji abruptly stood up and spun around. Bringing the handgun to bear, he raised it and fired.

**BLAM!**

The bullet tore into Asuka's throat, destroying her trachea and esophagus. Asuka's eyes widened in horror as she tried to stop the flow of blood coming from the wound. She choked to death on her own blood, as everyone watched in horror.

"Ikari..."

Shinji's head turned towards Rei. For the first time in her life, shock was the dominant expression on her face. Then Shinji calmly aimed his gun at her and fired.

**BLAM!**

The nine millimeter parabellum round drilled a perfect hole right between Rei's eyes, the window behind her shattering as the bullet exited the body, leaving a fist-sized exit wound in the back of her head.

As Rei sank to the floor, Shinji turned on his classmates as they tried to flee.

* * *

The call had came in minutes later. A shooting at Tokyo-3 Junior High School. Class 2-A.

Almost immediately, Misato, along with Ritsuko and Fuyutsuki rushed to the school. Gendou, of course, had remained behind.

Upon arriving at the scene, they saw that it was one of chaos. Numerous students injured, most of them were from being trampled as the school evacuated. But some of them were gunshot wounds. Section 2 was also present, doing a good job of keeping the press away from the scene.

Misato saw that one of the injured were Kensuke. He had caught a slug in the shoulder. Hikari was catatonic, having seen her friend being brutally murdered. He was being treated for his injuries in the back of an ambulance. Touji was there. Luckily, the bullet he caught had struck the prosthetic leg.

"What the hell happened here?" Misato demanded once she had reached the crippled jock and the injured otaku. "Aida...Suzuhara...what happened here? Where are the others?"

"He killed them," Kensuke whispered. "He killed them."

"What? What's he saying?" Ritsuko demanded.

Misato ignored Ritsuko for the moment. "Who, Aida? Who killed them?"

"Asuka kept prodding him," Hikari whispered. "Kept provoking him...we all did...Shinji...he...he..."

That was all she managed to say before pointing over to three bodies that were on the ground, each covered with a white blanket, Fuyutsuki talking to a trio of Section 2 agents, one of them handing him something in a plastic bag. Feeling a growing sense of dread in her gut, Misato walked over to the bodies, followed by Ritsuko.

"Sir?" Misato began.

Fuyutsuki looked even older than he really was when he gave them the bad news. "The Third Child had executed both the First and Second Children." He then raised the item in his hand. Misato blanched.

It was her handgun, inside an evidence bag.

"Oh, God," Ritsuko whispered.

"Is this your gun, Major?" Fuyutsuki asked.

Misato nodded. "It...I thought I had misplaced it, sir," she admitted.

"From what I managed to find out," Fuyutsuki continued, "Sohryuu had been harassing Ikari for the past month since his return from Unit One. Ikari had simply reached the breaking point and had murdered both Sohryuu and Ayanami, and injured at least five more people before turning the gun onto himself."

He turned to the three agents guarding the bodies and gave them a nod. They pulled the sheets back, allowing Ritsuko and Misato to identify the bodies. Sure enough, the still forms of Rei Ayanami, Asuka Sohryuu and Shinji Ikari greeted them. Each had gunshot wounds; Rei in the head, Asuka in the throat, and Shinji's self-inflicted wound on the temple.

Ritsuko paled. She knew that part of the blame was on her shoulders, as it was on everybody else since the Dummy Plug fiasco. The signs of Shinji snapping were there, but they refused to help him, after all he had done for them. They had branded him a coward, not realizing that they had led him down this path of self-destruction.

Now, it was too late.

Without the pilots, the world was screwed.

With the arrival of Arael, Third Impact was initiated. The world had all but ended.


	4. Episode 3: First Blood and Vengeance

_**Episode 3: First Blood and Vengeance**_

Snafu's Notes: I kinda goofed on the timeline. Snake is called out by Big Boss in 2013, not in 2012. It is then that Seele attacks the facility. Oh, and part of the story is done in MGS fashion.

Snafu's Notes, Pt. 2: The Beauty and Beasts Unit make their debut!

FOXHOUND Training Facility – near Seattle Washington.

In the chaos that was Second Impact, the city of Seattle, Washington had managed to survive the chaos that was Second Impact pretty much intact. Originally considered to be the new home of the United Nations before pulling out its bid and allowing Tokyo-2 to win the bid.

It was home, however to the newly-reformed Special Forces unit, codenamed FOXHOUND.

The location of the facility was that of an industrial warehouse, located on a small airfield, about the length of a football field, complete with a training area, workout center, firing range, laboratory for research and development, and a nearby hangar where FOXHOUND's main mode of transport - the modified C-17 Globemaster III which was christened The Nomad - was at the moment, parked.

* * *

At the moment, FOXHOUND's second-in-command (and squad leader of Rat Patrol One) was strode down the hallway with a purpose. Short scarlet hair, piercing green eyes, dressed in the short-sleeved khaki uniform that served as the summer uniform of FOXHOUND. She held the rank of Major, as it was noticed by the gold oak leaf insignia on her collar. The hip holster contained her signature weapon – a matte-black, Mark VII Desert Eagle.

The name tag read** CAMPBELL**, having taken on her father's surname in honor to his memory.

Stopping in front of a door whose sign read **FOXHOUND COMMANDER**, along with the second sign which read **ABANDON ALL HOPE, YE WHO ENTER HERE**, she knocked on the door.

"Come in," the voice of the FOXHOUND commander spoke from the inside.

The gun-toting Shadow Moses survivor entered the office. Along with the FOXHOUND commander, one other person was present. He was known as one of the two computer geniuses FOXHOUND had on payroll, Doctor Hal Emmerich. Seated behind the desk, dressed in FOXHOUND khakis, the rank of Colonel evident on his collar, the bandanna absent, was the current commander, Solid Snake.

The hair was shorter, but there was no denying the fact that it was him.

"Scarlet Fox," Snake greeted, calling Meryl by her codename.

Meryl Silverburgh-Campbell nodded her head in greeting. "Gentlemen," she responded.

Snake acknowledged his subordinate with a nod. Motioning Meryl to come closer, Snake gestured to the laptop on his desk – apparently Otacon's since the Policenauts sticker attached to it was a dead giveaway.

"Looks like the old man has finally made his move against Seele," Snake said. "We got the video feed from the RAYS when they attacked the Tarumae facility. Otacon?"

The bespectacled man nodded. Punching in a couple of keys, he spun the laptop around, allowing Meryl to look at the video. Needless to say, Meryl was impressed.

"Good thing those RAYs are on our side," Meryl noted. Pausing for a moment, she turned to Snake. "Permission to speak freely, Colonel?"

"Granted," Snake replied.

"Can you really trust Big Boss, let alone Ocelot?" Meryl asked, still skeptical of the alliance between FOXHOUND and the reformed Patriots.

"Given what's at stake here," Snake replied, "I'm willing to give Big Boss the benefit of the doubt. Then again, Zero and the original Patriots have used me to infiltrate Outer Heaven and Zanzibarland and screw Big Boss over. And that incident two years ago..."

Meryl stiffened at that remark. She remembered that incident all too well. Two years earlier, Seele, seeing the reformed Patriots' power as a thread for their plans for Instrumentality, tried to have the Patriots killed, using a PMC they had on their payroll. Snake and Meryl were there at the time, and had retreated along with Big Boss and the others, but there were two casualties in the ensuing gunfight.

Roy Campbell, Meryl's father and the former commander of FOXHOUND, and EVA, Big Boss' faithful consort.

Snake had seen Big Boss pissed before, and with the deaths of his longtime friend and lover, he knew that the old man would be out for blood. Namely Seele's.

In the months following the Manhattan Incident, Snake had rejoined Meryl. Aiding Raiden, the trio rescued Olga's newborn daughter from the Patriots. As to the question of who would raise little Sunny, Rosemary volunteered, adopting the young girl and raising her as her own, along with Raiden.

For the past decade, Snake and Meryl had tiptoed around the idea of having an actual relationship. They dated on-and-off for the past decade. But mostly, Snake had taken Meryl on as his student in CQC. Needless to say, Meryl was a talented student.

"So what happens now?" Meryl asked. "Do we just sit here and wait?"

Snake shook his head. "No. Knowing Big Boss, he will call. When the time comes, we'll be ready. From what Otacon got from the scrolls, there should be at least two Angels left. Then Seele will make their move in trying to take over Nerv, since Ikari now holds the key to unleashing Third Impact. We can't let that happen. Too many lives were lost when Seele triggered Second Impact."

Snake wasn't no fool. His high IQ bear witness to that. But since Second Impact and the start of the Angel Wars, even the solider known to make the impossible possible found his foundations rocked to the core.

"Otacon."

FOXHOUND's resident otaku turned to his longtime friend. "Yeah, Snake?"

"When will the new Sneaking Suits be completed?" Snake asked.

Otacon pushed his glasses up on the bridge of his nose. "Well, we just got to see if the OctoCamo works, and that should take about a week."

"Anything else?"

"Just that Wolf's battlesuit upgrade will take an extra couple of days, but that should be no problem."

Snake nodded. "Both you and Mei Ling finish up on the suits. Once these last two Angels are destroyed, Big Boss will call us in to help. With Seele losing their main advantage, they will surely move to invade Nerv Headquarters once the Angels are defeated."

Otacon nodded.

"Dismissed," Snake said.

Once the office was cleared, Snake leaned back into his chair and sighed. Things had become very hectic in the past couple of years following Outer Heaven, Zanzibarland and more importantly, Second Impact. The last thing he expected was to run the special forces unit that his father had built.

Father...Snake never really could call Big Boss that. He had his reasons. Liquid and Solidus did, but not him. The events which led him to assume command of his old unit began two years ago...

* * *

[Flashback]

Two years earlier, A.D. 2013...

Following the Manhattan fiasco, Philanthropy continued its work, tracking down duplicate copies of Metal Gear. As time passed, however, the nations of the world had decided that rebuilding the world from the ashes of Second Impact was a lot better than creating weapons of war. Thus, the number of Metal Gears dwindled, until there was none.

During this time, Snake had caught up with his old flame, Meryl. Since Shadow Moses, she had been working with the Army's Criminal Investigation Command, trying to track down the Patriots. Like Snake and Otacon, she had reached a dead end. Raiden, in the meantime, had reconciled with Rosemary following Manhattan. At Rose's suggestion (or urging, depending on your point of view), Raiden sought psychiatric help. In between visits to the shrink, he and Snake had tracked down Olga's child and had rescued it from the clutches of the Patriots. The former child soldier known as 'Jack the Ripper' and Rose decided to adopt the child as their own, with Snake and Otacon acting as uncles, while Meryl and Mei Ling played the doting aunts.

Mei Ling continued to work for the Army's Soldier Systems Center, although she had toned down her activities in obtaining the items needed for Snake and Otacon to continue their war against the Gears and the Patriots.

Then one day, while visiting Raiden, Rosemary and Sunny, Snake received a call on his CODEC. A call from someone he did not expect.

"Snake. We have unfinished business. Come outside."

Naomi Hunter.

The former chief medical officer of FOXHOUND during Shadow Moses. The younger sister of Gray Fox, who had died in that same place.

With his pistol loaded and tucked behind his back, Snake stepped outside. Sure enough, Naomi stood there, waiting for him. Behind her, was a parked sedan, the windows tinted. Snake made his way towards the exotic beauty, still apprehensive, still on his guard. After Shadow Moses, he did not really trust Naomi, after what she had done to him in the name of vengeance. When he got within double arms' reach, he stopped. Back on the porch, Raiden and Meryl watched, weapons at the ready, should Naomi tried anything.

Naomi didn't waste any time. "I want the truth, Snake," she said calmly. "I want the truth about Frank."

That caught Snake off-guard. Of course he knew that Frank was the one who had killed her parents during the Rhodesian Civil War, but spared her out of guilt. Frank had told him while in Shadow Moses. Following the mission, Snake relented from telling Naomi.

It was a confession, released in the midst of battle against Metal Gear REX. When Snake demanded that Fox should stop Naomi, Frank dropped the bomb on his former comrade.

_"Because I was the one who killed her parents. I was young then, and I couldn't bring myself to kill her too. I felt so bad, that I decided to take her with me. I raised her like she was my own blood, to soothe my own guilty conscience. Even now she thinks of me as her own brother...From the outside, we might have seemed like a happy brother and sister. But every time I looked at her, I saw her parents' eyes staring back at me. Tell her for me. Tell her that I was the one who did it."_

Snake sighed. Naomi deserved closure.

"He told me, back in Shadow Moses," Snake began. "We were taking cover from REX and he told me. He killed your parents back during the civil war in Rhodesia. But he could not kill you, because of the guilt. He took you with him to raise like a little sister. I purposely held back because you loved him so much, that you were even willing to take revenge on him by killing me."

Silence reigned for a moment, Snake allowing Naomi to digest this information.

"Snake...thank you...for telling me the truth," Naomi said. She then pulled out a item from her pocket and tossed it to Snake.

Snake caught the item and inspected it. It was a syringe, labeled FOXALIVE.

"It will cure you of the FOXDIE that is in your system," Naomi explained.

Snake looked at the syringe, then back at Naomi. "How do I know that this isn't going to kill me?" he asked.

Naomi produced a second syringe, only this one was red. "Because this one would have killed you," she said before pocketing the item. She turned to leave, but stopped and turned around. "One more thing. Go to Prague. Someone wishes to speak with you. Look for a church in the old part of town, and ask for Big Mama. It concerns **him**."

With that, the meeting was over. Naomi stepped into the passenger side and the sedan peeled off.

* * *

Prague, Czech Republic – several days later.

Following Second Impact, most of Eastern Europe was caught in the civil wars that had engulfed the world. Following the Valentine Treaty, things had calmed down. With a new military government in place, order was restored in the country. The military government also kept a tight leash on who could and could not enter the country.

However, luck was on Philantrophy's side, since a friend of Otacon's worked with the military government. At the moment, the Nomad was parked on a runaway.

Inside the plane, Snake and Meryl were going through the parameters with Otacon. Snake was clad in his Sneaking Suit – the same one he wore during the Manhattan mission – while Meryl was dressed in her own battle dress uniform (i.e., her Rat Patrol 01 uniform). As it turned out, Naomi was as good as her word. After Snake had injected himself with the syringe, the following physical showed that his body was free of FOXDIE.

"I managed to clear it with the Czech government," Otacon explained as he watched the two prepare. "We can stay in the country for 36 hours. After that, we got to leave. Remember, we're here to find Big Mama, hear what she has to say, then we get the hell out of here. The Czechs already dislike foreigners, Americans especially. From what I managed to find out, there's been some serious activity inside an abandoned church located in the old city. Rumor has it that Big Mama's hiding there. But the church is heavily guarded by her private militia, war orphans and a small number of vets who survived Outer Heaven. Which is why you're going to be using the stealth camouflage, since there are armed patrols by the Czech military."

"Got it," Meryl said as she holstered her Desert Eagle.

"Good luck, the both of you," Otacon said.

"Thanks," Snake replied as he and Meryl activated the camos and departed from the plane.

Despite the stealth camo, Snake and Meryl stayed close to the shadows. It took them about an hour, but they soon reached their destination – a cathedral. Built in the grand design of Gothic architecture, it was closed for renovations – a perfect cover for someone who didn't want to be discovered. Of course, getting in was a completely different story. The only way in was by using a numeric code, one that Snake nor Meryl did not have on hand. That problem was rectified when Snake and Meryl noticed someone walk up to the front door and punched in the code. Snake was on him in an instant. Of course, it had negated his stealth camo once he touched him, but Snake was one who did not worry on small problems.

With the guy's arm twisted behind his back and his own arm secured around his throat, Snake forced his way in, followed by Meryl, still in her stealth camo. Seconds later, Snake found himself surrounded by three armed men.

"I'm here to see Big Mama," Snake declared, still behind his human shield.

"Is this him?" one of the armed men asked.

"That's him all right," the second man replied.

"I...I didn't hear him coming," the human shield managed to croak out.

That was all that was said, before Snake took down those three men, plus five more with his CQC, the last one Snake punted through a set of double doors, sending him into the sanctuary, where he landed in a heap in the center aisle.

Another soldier tried to get the drop on Snake, but was dropped himself, as Meryl clocked him with her Desert Eagle, smacking him in the back of his head, knocking him out. She deactivated her camo and followed Snake inside the sanctuary.

Inside, standing at the altar (in her MGS4 get-up), was an elderly blonde woman. Standing beside her, was Naomi Hunter.

"You CQC is most impressive, Snake," the old woman complimented, arms folded. "You truly are the one who makes the impossible possible."

Snake lowered his gun, but kept it drawn. Meryl did the same. "You're Big Mama, I presume?" Snake asked.

Big Mama, otherwise known as EVA, nodded. "I am," she admitted. "You've grown, David."

That caught Snake off guard. She knew him by his real name. "You know me?"

"I should. I was the one who gave you life," EVA replied. "I'm your mother."

Snake looked like as if he had been gut punched Meryl also looked flabbergasted as well.

EVA decided to explain. "The Les Enfant Terribles Project. You can't grow a human being in a test tube. Not even a clone. You need a woman's body to give it life."

"A surrogate mother," Meryl snorted.

Eva did not look offended. "That's an awfully cold way to put it, but yes. Either way, I gave birth to you...and for the Patriots."

"Forgive me if I seem skeptical," Snake declared. "But I find this hard to believe."

"It's true, Snake," a second voice said from the shadows. "She's telling you the truth."

Snake blinked, as did Meryl. 'No...it can't be...' they both thought at the same time.

The man stepped out from the shadows. He was no longer in uniform, but rather a formal business suit. He was also leaning on a walking cane.

Snake recognized him instantly. "Colonel Campbell?"

Roy Campbell nodded. "It's been a long time, Solid Snake," he greeted. Turning to Meryl, he simply said, "Meryl."

Meryl nodded in greeting. "Dad."

In the years following Shadow Moses, Meryl had come to terms that she was the end result of the affair between her mother and Roy Campbell. Growing up, she always thought of the old man as her uncle. But since losing her mother in Second Impact, Meryl had made an attempt to reach out to her estranged father.

So far, it had worked.

"What are you doing here, Colonel?" Snake asked.

"It's kind of complicated," Campbell admitted. "But you should listen to Big Mama. She came to me and explained what was at stake. In the end, I decided to join up with her."

Snake looked at Campbell for a moment. "Okay, Colonel. I'll bite."

Campbell turned to EVA and nodded.

EVA laid it all down. Operation Snake Eater, Les Enfant Terribles and her role in that secret project, and her relationship with Snake's father, Big Boss. It did answer questions that Snake had in regards to some questions in regards to his origins. But EVA kept back from answering certain questions about his past and that of the Patriots.

It was then, Snake and Meryl received shock number two.

Snake's intuition snapping into overdrive, he shoved Meryl out of the way and hopped back, just as the gunshot went off, the bullet striking at Snake's feet. Meryl rolled along the ground, stopping to retrieve her Desert Eagle, Snake brandishing the Operator.

"Well, well, well," an old voice said. "Isn't this the big reunion...shadows of Shadow Moses, isn't it, Snake?"

Watching from the sidelines as Ocelot appeared, his dual revolvers drawn, EVA, Naomi, and Campbell were not all that happy. They wanted to get Snake and Meryl on their side, and given Snake's past with Ocelot, that would not be easy.

It was a standoff. Ocelot had his revolvers drawn, aimed at both Snake and Meryl, the former with his Operator drawn, while the latter had the gunslinger in her sights with her Desert Eagle.

"Ocelot..." EVA drawled. "You promised to behave. Holster your weapons."

"When these two lower their weapons, I will lower mine," Ocelot replied, guns still raised.

"Goddammit, Ocelot! Holster your guns now!" Campbell shouted.

"I don't take orders from you, Chicken Fox," Ocelot snapped, calling the former FOXHOUND commander by his former codename.

"No. You take orders from **me**," a fourth voice - just as old as Ocelot's - said. "Holster your weapons."

It had been years since Zanzibarland, but Snake recognized that voice in an instant.

He then came into view, appearing from the back room near the church's altar. The footsteps echoed throughout the church as he walked along the hardwood floor. Ocelot, in the meantime, holstered his revolvers.

There was no denying it now. Six feet, two inches tall, the white hair combed back, the beard trimmed. The ever-familiar black eyepatch covering his damaged right eye. The olive green officers' uniform which had no rank – not that he needed one, since everyone knew who he was, the uniform partially concealed by his khaki FOXHOUND-issue trenchcoat.

Last, was his signature weapon – the modified Colt XM-16E1 with the shortened barrel and the removed stock, known as the Patriot – held in his right hand.

"It's been a long time, Snake," Big Boss drawled.

Snake's aim faltered slightly. "Big...Boss?"

Meryl blinked. She was facing a legend. The same one that Snake had defeated when she was a child. "Big Boss? The Big Boss? Are you sure?"

"The one and only," Ocelot said as he backed up to where Naomi, EVA and Campbell stood.

Big Boss raised the Patriot as he resumed his slow advance. Snake had the gun raised in an instant, prepared for anything. He knew that Big Boss was deadly with that weapon. Meryl decided that discretion was the better part of valor and backed off. When the old man got within five feet of Snake, he stopped.

Then he lowered his gun.

Snake breathed out a sigh of relief.

Then, after taking two steps, Big Boss raised the gun with one hand, slowly and deliberately, until he had it aimed at Snake's chest, forcing Snake to raise his own gun.

Then Big Boss did something that Snake wasn't expecting.

He dropped the Patriot, where it landed on the floor with a clatter. It also distracted Snake long enough for Big Boss to make his move.

Snake had just lifted his ban on practicing CQC, and was pretty rusty. Big Boss, however, had never stopped practicing. In under five seconds, Big Boss had disarmed Snake and had the younger man flat on his back, the Operator in his gloved hand.

"Let it go...my son," Big Boss said calmly, as Meryl helped Snake to his feet. "I'm not here to fight." Gripping the Operator by the barrel, he extended the weapon to Snake. "Or should I call you...brother?"

"How...?" Snake began.

"Simple," Big Boss replied. "That was a decoy who you have killed back in Zanzibarland. I had been in Japan the whole time, recovering from Outer Heaven. I'm not as spry as I was when I was younger."

Snake reached out and gripped his pistol. Holstering it, he knew that Big Boss held his attention.

Big Boss looked at Meryl. Without turning around, he addressed Campbell. "Your daughter?"

"Yes," Campbell admitted.

"Hmm. Looks like you," Big Boss mulled. He then turned back to Snake. "I guess I should start from the beginning, so that you can understand. It all began with a bunch of old fools. Now...most of them have passed away. Their era of folly is over. Ocelot...EVA...and myself...we're the last. The last of the original Patriots."

"The Patriots?" Snake repeated. "You're one of the members?"

Big Boss nodded. He explained everything. From the Philosophers, to the formation of the Patriots, to Big Boss' departure and later open rebellion against Zero. Snake wasn't very happy to being used as a pawn in Zero's game. For many years, he thought that Big Boss was a traitor. Now, everything was clear. Big Boss was no traitor.

He wanted to simply free himself from Zero's intentions. Big Boss also came to terms about his own faults regarding Snake and the Les Enfant Terrible project.

"I've never thought of you as a son," the old man admitted. "But I've always respected you as a soldier. And...as a man. If you'd been in my place back then maybe you wouldn't have made the same mistakes that I did. Ever since the day I killed The Boss with my own hands...I was already dead."

A sad smile spread across Big Boss' face as he remembered his mentor. "Boss...you were right. It's not about changing the world. It's about doing our best to leave the world the way it is. It's about respecting the will of others... And believing in your own. Isn't that what you fought for? At last...after all these years...I understand the meaning behind what you did. At last... I understand the truth behind your courage."

"It was you, wasn't it?" Meryl asked. "You were the one who blew the lid off of Operation Snake Eater? You got The Boss the posthumous pardon from both the U.S. and Russia, right?"

"It was the least I could do," Big Boss replied.

"And you got Otacon and myself cleared as well, right?" Snake said.

Big Boss nodded as he retrieved his Patriot. "There was another reason why I called the both of you here," he continued. "With the deaths of Zero, Signt and Para-Medic, and the destruction of the Patriots' AIs and their proxies, the Patriots have a new leader...me. But...as much as I would like to unite the world, we first must defend it."

"Defend it? What are you talking about?" Snake asked.

"You are familiar with the event on 13 September 2000?" Big Boss asked.

[Scene fades out to that of footage of Evangelion. Mainly, Second Impact. ADAM's Wings of Light are spread as disembodied souls surround him.]

SNAKE: (voice-over) You mean Second Impact, right?

BIG BOSS: (voice-over) Correct. It was not caused by a meteor crashing into the South Pole at light speed. Second Impact was man-made...and deliberate.

[Scene shifts to ADAM under Mount Markham. The Katsuragi Expedition has discovered him.]

BIG BOSS: (voice-over) There was something there, underneath Mount Markham. A being known as the first of Earth's Seeds of Life, codenamed ADAM. ADAM was discovered by the Katsuragi Expedition in early 2000. But something went wrong as the expedition team researched their find. The experiment was sabotaged, and ADAM, for lack of a better term, exploded. The explosion melted the ice caps and triggered the mega tsunamis that laid waste to the Southern Hemisphere.

MERYL: (voice-over) Who...who was responsible for this?

[Scene shifts to the twelve monoliths that consists of Seele.]

EVA: (voice-over) A powerful entity known only as Seele. They control the United Nations, pulling the strings from behind the scenes. From what I found out, they've been around since World War II, as a rival to the Philosophers. When the Philosophers splintered due to the Cold War, they gained power. In 1947, the Dead Sea Scrolls were discovered. Within those pages were a segment called the Secret Scrolls.

[The clips end here. Back to the story...]

Big Boss turned to Ocelot and nodded. The old man reached into his pocket and retrieved a flash drive. He tossed it to Snake, who caught it. "The information is on that drive. I'm sure that Dr. Emmerich would be most interested on what's inside. Like father, like son."

"You knew Otacon's father?" Snake asked.

Big Boss nodded. "Yes. We met back in Costa Rica nearly thirty years ago. Back when I was the commander of Militaires Sans Frontières."

"Seele's intentions are to unleash a Third Impact upon the world," Ocelot said. "If you thought Second Impact was bad, then Third Impact is far worse."

"Third Impact?" Snake repeated.

"Seele believes that humanity has reached its peak and is stagnating," Ocelot explained, "and wishes to use Third Impact to achieve Human Instrumentality And despite the world having its faults, humanity is worthy of survival."

"Basically, Third Impact is the end of the world," Big Boss said. "Second Impact will look like a firecracker compared to what will happen if Seele succeeds. Which is where we come in. Only problem is despite the financial reserves from the Patriots' funds and what's left of my personal reserves, we lack the manpower. My influence is that of the American government and military, as well as the Japanese forces. But even that is not enough. I want people that I can trust."

"You're asking us to join up with you?" Snake asked.

Big Boss nodded. "Yes."

* * *

[End Flashback]

'I guess it had taken a lot of willpower to call me out like that,' Snake continued as he continued to think back. 'And now he's the leader of the Patriots...I guess I must be out my mind when I actually decided to join him.'

When Big Boss had made his peace with his remaining son (or clone, depending on your point of view), he gave Snake an offer: join the Patriots and help defend the world against Seele. Before Snake could give Big Boss his answer, the church was under attack.

Seele, deciding that Big Boss and the Patriots were a credible and deadly threat for the plans for Human Instrumentality, had decided to strike. Using a contact within the Czech government, Seele had found out where the reformed Patriots were hiding, and decided to strike.

Seele's primary military arm was a PMC known as the Haven Shock Troops. Nicknamed FROGS because of their superhuman acrobatic and athletic abilities, the Haven Shock Troops were an elite, all-female, men-hating, and incredibly deadly military force consisting of three highly-trained combat combat units. In the wake of Second Impact, they became known for their ruthless campaigns throughout the Southern Hemisphere. That ruthlessness had caught the attention of Seele, who retained them for several covert campaigns all over the world, eliminating those who had exposed the truth concerning Second Impact, killing their friends and families.

EVA's personal 200-man guard, called Paradise Lost, held them off as they made their escape. Much to Snake and Meryl's surprise (aside the fact that they were on the same team as Ocelot and Big Boss), was that Campbell was holding his own in the firefight.

* * *

[Flashback]

Gunfire erupted from the inside of the church as Big Boss, Campbell, EVA, Ocelot, Naomi, Snake and Meryl made their retreat. The church had a rear parking lot, where several motorcycles were parked, along with a military-grade Humvee complete with a 50-caliber gun mount.

One of the Paradise Lost members ran up to EVA and Big Boss. "Big Boss! Big Mama! This way! We will cover your escape!"

"Never thought that Seele would do something like this," Ocelot muttered as he reloaded his Single Action Army.

Campbell reloaded his own Beretta. "They caught us with our pants down. We need to get out of here."

"On it," Meryl said. Activating her own CODEC, she hailed Otacon on the Nomad. "Otacon, it's Meryl! Get the Nomad ready! We're coming in hot! ETA is ten minutes! And we're bringing company!"

"Understood," Otacon's voice replied.

"You five, in the Humvee," Big Boss ordered.

As Snake, Meryl, Naomi, Ocelot and Campbell piled into the vehicle, Campbell behind the wheel, Ocelot riding shotgun and Snake manning the 50-cal and Meryl and Naomi in the back seat, Big Boss walked over to EVA, who was starting up her motorcycle – a Triumph motorcycle, pre-Impact model.

"Just like old times, huh, Jack?" EVA said as she relished in her newest toy.

Big Boss settled in behind her, one hand around her waist, the other still holding the Patriot. "Been a while since I went on a ride with you."

EVA smiled, a moment only for them in the middle of a gunfight. "I told you once before, Jack," she said as she gunned the engine.

"I know," Big Boss said, returning the smile. "You'll only get off your bike only if you either fall in love or fall dead."

EVA pulled up to the Humvee. Big Boss turned to Campbell. "Reminds me of the first time we met back in San Hieronymo. Good to see you're still good at what you do. Follow us to the airport. Snake got you covered."

Campbell nodded. "No problem, Boss."

Just then five FROGS came charging into the parking lot. Brandishing Belgian-made FN-P90s loaded with armor-piercing rounds, they opened fire on the remaining members of Paradise Lost. They, however, did not last very long against Big Boss and his trusty Patriot. Nine more came out, only to be dispatched by the gun mount atop the Humvee.

EVA gunned the engine on her Triumph. "Let's go!"

She peeled off on her bike, the Humvee close behind.

Following a high-speed chase through the deserted streets of Prague, the six survivors arrived at the airport, with Seele's forces hot on their heels. During the chase through the empty streets, along the canal road, a FROG sniper had fired upon the Humvee, nailing Campbell in the chest. Snake spun the turret around and riddled the sniper with bullets.

Campbell was still alive, but the round from the sniper's rifle had caught him in the lung. Naomi applied medical aid and was able to stop the bleeding, but even she could see that his chances of survival were low. However, EVA had planned something like this, and had acted accordingly. One of the bridges was rigged with C4 and after crossing it, Ocelot had detonated it, destroying the bridge, thus forcing their pursuers to take the long way around.

Finally, they had reached the airport. Seconds later, two vans containing ten armed men appeared. Snake turned his 50 caliber upon one of the vans, and was able to destroy one of the vans before running out of ammo.

The Nomad's ramp was down, Otacon standing in front of the plane as the Humvee and the bike screeched to a halt.

Snake hopped down from the gun mount and provided covering fire, while Meryl and Naomi helped the injured Campbell on board. "Otacon! We are leaving! Now!" she shouted.

"Got it!" the resident otaku nodded. His eyes widened at the sight of not only Ocelot, but also Big Boss himself.

"Move!" Ocelot barked, forcibly spinning Otacon around and shoving him up the ramp.

Big Boss and EVA provided covering fire as the others boarded the plane. The arriving FROGS were forced to take cover from Big Boss and his Patriot, ducking behind cars.

EVA's Mauser clicked empty. As she retrieved a fresh clip, she saw that one of the FROGS had attempted to flank her and Big Boss's position. Big Boss was distracted with gunning down two of the shock troops, but EVA saw her coming.

She shoved Big Boss out the way, just as the gunman fired, EVA cried out as the bullet punctured her chest.

"EVA!" Big Boss screamed, right before training the Patriot upon the gunman, the rounds from the modified Colt spinning end over end, catching the unfortunate assassin. He was dead before he even knew what had happened.

Big Boss tossed the Patriot to Ocelot. He then scooped the injured woman into his arms and carried her on board The ramp closed and the Nomad made its way onto the runway. More gunmen had arrived on the scene, but it was no use. The Nomad had escaped.

* * *

30 minutes later, the Nomad was out of Czech airspace. Naomi, with Snake acting as her de facto assistant, was hard at work, trying to save the lives of both EVA and Campbell. But it was no use. The wounds they had were indeed mortal. Even Snake knew that there was no hope. So despite their circumstances, Naomi had tried to make their last moments comfortable.

Roy had died first. Meryl was so wracked with grief that Naomi had to sedate her.

Big Boss was at EVA's side. The old woman was resting on a cot, with her longtime companion watching over her in a silent vigil.

"Jack?" EVA whispered, her eyes slowly opening. She did not have long.

Big Boss gently clasped his mate's hand. "I'm right here...my love."

EVA smiled weakly. She knew she was dying. This part of Big Boss - the side where he was not a soldier - was for her alone. "Jack...can you do something for me?"

"Anything...Cynthia."

EVA caressed his bearded face. "Kiss me...one last time."

Big Boss complied. He kissed EVA for the final time. Then she took her last breath and her body was still.

EVA was gone.

Then Big Boss did something that no one had ever seen him do.

A single tear escaped from his eye as his shoulders shook with every sob he made.

Big Boss was crying.

* * *

Six days had passed since their escape from Eastern Europe. During this time, a funeral was taking place, in Arlington National Cemetery.

Roy Campbell's funeral.

He was buried in his officer's uniform and beret, with full military honors. Snake, Meryl, Otacon, Raiden, and Mei Ling were in attendance, along with three more people.

Naomi Hunter, Revolver Ocelot, and Big Boss.

The three had arrived together, Ocelot and Big Boss in full uniform, complete with berets given the fact that Ocelot himself was a former FOXHOUND member and Big Boss himself, was the founder of the unit, while Naomi wore a black mourning dress.

Raiden took one look at Big Boss and was about to go for his service pistol, until Snake ordered him to stand down. "It's not Solidus, Raiden," he said. "Solidus had the eyepatch over his other eye, remember?"

"Then...who...?"

"It's Big Boss, the founder of FOXHOUND," Snake explained. "And...my father."

"And Ocelot?"

"Long story, but all I can say is that Ocelot and Big Boss worked together since Operation Snake Eater."

Once Big Boss had paid his respects to his fallen comrade, he did not leave the graveyard. Instead, he moved on to a second headstone not too far from where Campbell was being buried, as did Ocelot. Naomi had decided to wait near the sedan.

Once the funeral was over, Mei Ling led Meryl to a waiting car, while Snake, along with Otacon and Raiden, followed Big Boss and Ocelot to the other grave.

A grave which Solid Snake recognized.

The grave of Big Boss' mentor, The Boss. The headstone had been replaced, but it still bear the same epitaph, just slightly modified; **IN MEMORY OF A PATRIOT WHO SAVED THE WORLD - BORN: 1920 DIED: 1964.**

Big Boss placed a bouquet of flowers along the headstone, as did Ocelot. The two old men snapped into attention, before raising their right arms in a salute, showing deep respect towards the woman who was the driving force behind both their lives, before dropping the salute.

"We were betrayed by a senior member of the Czech government," Big Boss explained without taking his eyes off the grave. "Ocelot found him while he was in Germany and he explained everything."

"He also died very, very painfully," Ocelot added, a sadistic grin on his face.

"Otacon checked out the flash drive," Snake said. "Looks like you were right about everything. You're going after Seele, aren't you?"

Big Boss nodded. "I owe it to EVA and Roy," he replied, his face grim.

"I want in," Snake said. "We all do. Roy was not just my former commanding officer. He was my friend."

The old man turned to Snake. "I had a feeling you would, son. Welcome to the Patriots."

"So what's the plan?" Snake asked, following Big Boss and Ocelot to the parked cars.

"We wait," Big Boss replied. "We got two years before Seele hatches their scheme for Instrumentality. I hope by that time, the next-generation RAYs will be completed."

"Wait...you're constructing RAYs?" Otacon said. "Why?"

Big Boss responded to that question. "Simple, Dr. Emmerich. By using the power of Metal Gear, it will even the playing field, so to speak. Think of them as our ace-in-the-hole."

"How many are you constructing?" Snake asked.

"Three. At the moment, they are being constructed at the old Shadow Moses facility," Ocelot said. "Seele thinks that they have destroyed the Patriots, so we have the advantage."

"I will be heading back to Japan," Big Boss explained. "I got some friends from Outer Heaven who are top brass within the JSSDF. I'll be working as a analyst with the U.N. armed forces."

"What about us?" Snake asked.

"Easy. One year from now, FOXHOUND will be officially reactivated...and I want you to lead the unit," Big Boss said. "FOXHOUND will be a special forces unit under the jurisdiction of the U.S. Army and the C.I.D."

"So you want us to check things out stateside, right?" Snake asked.

Big Boss nodded. "There's several facilities that Seele uses for their operations. Then there's Nerv, which is financially backed by Seele. The RAYs will act as a buffer to the EVAs. Naomi is already working at Nerv as a psychologist and doctor. If you want to get in touch with me, contact her. Understand?"

Snake nodded. "Crystal." When Big Boss and Ocelot turned to leave, Snake stopped him. "Boss?"

Big Boss turned around.

"For what it's worth," Snake began, "I'm sorry for thinking the worst of you following Outer Heaven."

"I never was a traitor, David," Big Boss replied. "I'm...loyal to the end. That's my purpose."

Big Boss turned and departed from the scene, Ocelot behind him.

[End Flashback]

* * *

That was how it had all begun.

The last thing Snake had expected was to work for the Patriots, given how he had spent a number of years trying to expose them, only to find out that Big Boss, Ocelot and EVA had destroyed them.

Since then, FOXHOUND had grown. Meryl was the second person to join up, since Seele had taken away her parents; her mother had died while vacationing in Australia, one of the countries hit hard during Second Impact, and Seele had killed her father. After taking with Raiden about it, Raiden also agreed to work for Big Boss. Mei Ling and Otacon joined up soon thereafter. With the Patriots' funds at their disposal, Otacon and Mei Ling had came up with some nasty toys for the team to use.

Meryl was the squad leader for Rat Patrol One, a three-man team which herself, and two veterans of the wars that had engulfed the world following Second Impact. Ed and Jonathan were two soldiers hand-picked by Meryl, since she served with them following Shadow Moses, and had personally vouched for them. Snake allowed Meryl control of her own three-person squad, a play on the word 'Patriot,' hence the name, Rat Patrol One.

Then there was the second unit. A high-tech, all-female unit trained by both Big Boss and EVA, and thus, came highly-recommended by the old man himself.

The Beauty and Beast Unit.

In the wake of Second Impact, Big Boss, EVA and Ocelot had traveled the world, working as freelance troubleshooters at the U.N.'s request. In their travels, they came across four young girls, each one of them not only sole survivors, but traumatized by the events they witnessed, and in some cases forced to take part of.

EVA had taken them to Europe, where the continent had survived Second Impact pretty much intact. In the years following Outer Heaven, EVA had worked with Big Boss in reintegrating former child soldiers and those suffering under intense post-traumatic stress disorder back into normal society.

Big Boss and EVA saw the potential that these women had, and began to train them in their mid-teens. Seeing as how the girls had lost everything due to the Haven Shock Troops, they would be perfect as their instruments of vengeance. Using the ultimate advancements in Patriots technology, they were outfitted with specially designed suits which turned them into incredible soldiers.

Each of them were the best at what they did, and answered to both Snake and Meryl, while they both answered to Big Boss.

"It's your move, old man," Snake muttered to himself. "And I hope for all our sakes you know what you're doing."


	5. Episode 4: Battle in Tokyo 3!

_**Episode 4: Battle in Tokyo-3! Sohryuu vs RAY**_

Rei Ayanami hated two things.

The first, people who insult the Supreme Commander of Nerv. The second, being confused.

Currently, it was the latter.

The object of her confusion? One Shinji Ikari.

At the moment, the First Child was inside her apartment, laid out on her bed, looking at the ceiling, thinking about the past events that had transpired.

She may not look like it, but Rei was very observant. She simply hid it underneath her cool exterior. Up until a month ago, following his return from Unit One's core, Shinji was in Asuka's words, 'a spineless baka.' Now, he was anything but. He was simply cold. In some cases, even colder than Commander Ikari. As if he had shut himself away following Zeruel. She was not exempt. After all, she did slap him and called him a coward when he had returned.

She watched as Asuka and most of the class had pretty much made his life hell, making him a virtual pariah in their classroom, while having the class wrapped around her finger, and she did not raise one finger to stop the abuse. She knew that he would simply roll over just to avoid confrontation. She watched as Ritsuko snubbed him and his father act even more colder towards him. And did nothing.

Until that day...

...the day that he had simply stopped giving a damn about the people around him. She was there when Maya had tried to apologize for using the Dummy System, and Shinji had sent her running away in tears. Aoba and Hyuuga also steered clear of him when they demanded that Shinji should apologize to Maya, and he told them off as well.

Day by day, he grew colder and colder towards the majority of the senior Nerv staff. The only exception was Fuyutsuki, Mr. Kaji, and Dr. Hunter.

Then came the day that Shinji had not only chewed out Dr. Akagi, he also denounced his father, severing the tie between father and son. As for her, Shinji simply ignored her, as if he was refusing to recognize her existence. She would have slapped him then, but when he stared her down, she was literally frozen in place.

And three days ago, when Asuka had confronted him...

Even Gendou was willed into submission by his own son. No one dared to step in to stop Shinji from maiming Asuka. Not Misato, not Ritsuko, not even herself.

The following day, she would arrive at school with bruises all over her face, the more prominent one was at her throat, where Shinji had nearly strangled her to death. When questioned about it, Asuka's reply was that she had a freak accident while undergoing synch training. Unknown to the students of Class 2-A, said accident was Hurricane Shinji.

It had pretty much irked Asuka to no end.

Asuka could have told the class what had happened, which would have sent the majority of the class after Shinji, but there was the little fact that it would violate the restraining order placed on her, which would get back to the Geofront, and she would be ejected from the active roster, if not fired outright.

Earlier that day, Asuka had cornered Rei on the school rooftop, where Shinji would usually eat lunch at. But he was not there. Hasn't been there since Zeruel. Asuka knew that Rei was the one that could basically expose her for the poser that she truly was, and had decided to act in order to keep Rei from revealing Asuka's deception.

* * *

[Flashback]

Tokyo-3 Junior High School, earlier that day.

The two female pilots stood facing each other. One, a pale-skinned bluehead with crimson eyes, the other, a hotheaded half-German redhead, battered and bruised from her ill-advised confrontation with the sole male pilot of the trio.

"What do you want, Sohryuu?" Rei had asked in her cool tone.

"What happened back in the Geofront...was a fluke," Asuka snapped. "That pathetic spineless baka got lucky."

"I would not call it luck," Rei replied. "You provoked Ikari, and he simply defended himself."

Asuka growled. "Listen up, you blue-haired bitch. You've done a pretty good job in keeping your mouth shut, and it would be better for you to keep it that way. I'm the best pilot here. Don't you forget that. I got the entire class against the Third Child. And I can do the same to you as well."

Rei's response was to simply walk over to Asuka, until she was within arm's reach of her. Her red eyes burning into Asuka's own azure orbs, the pale-skinned girl replied, "I do not respond very well to threats, Sohryuu. **Especially** after what I had found out during the battle at the Nerv facility in Matsushiro."

Upon seeing the look of shock on Asuka's face, Rei continued. "You were right, Sohryuu. It **does** benefit in being Commander Ikari's favorite. And what would happen if I released the footage of the battle to the students in Class 2-A, after you told them that you so valiantly tried to save Suzuhara? I think that their opinion of you would change once they see you put out of action in under five minutes."

"You...you wouldn't dare," Asuka hissed.

Rei smiled. Unlike the smile she gave to the two Ikaris, this one was...evil. "Like I said, I do not respond too well with threats. Especially from you, Sohryuu. If you think that I am bluffing, then you are free to call my bluff. I guarantee you that you will be on the first flight back to Berlin without Unit Two."

Seeing as how she had won, Rei had excused herself from the rooftop, leaving her steaming teammate behind.

[End Flashback]

* * *

'Shinji would have been proud of me,' Rei thought sadly. But she would never know, since after Zeruel, she had went along with the others in condemning Shinji in regards to his actions after Bardiel.

It was after Shinji's confrontation with Asuka that Rei had started to think. After questioning Maya and the male bridge bunnies, she discovered that the entire debacle was Gendou's fault. He was the one who ordered the Dummy System to be activated, thus nearly killing Suzuhara. She knew that the Commander was a cold person, but to order the Dummy System to be activated, and to wash his hands of the whole affair, putting the blame on his son?

Rei was starting to see the one person who she would die for in a different light. And it wasn't a pretty picture.

'This feeling...is this...regret?'

It was after reaching his conclusion that she decided to try and mend her relationship with Shinji.

Only problem was that not only did he transferred out of Class 2-A, but he had also moved out of Misato's apartment and into his own place on the other side of Tokyo-3. No one, aside from Kaji and Fuyutsuki knew where he was. And he never stuck around to hear the synch scores, since she viewed most of the Nerv staff with nothing but contempt.

So Rei went with another course of action.

She followed Shinji one day after school. Instead of heading to his new home, he instead, headed for the park. There, she found the reason why Shinji was able to defend himself.

The reason being was that Shinji was trained to do so by the old man. From the look of things, Rei deduced that he was military, given his uniform. The first time she followed Shinji, the old man was dressed in combat fatigues and a beret. From her hiding place, she watched as the one-eyed man defeated Shinji, but the boy did put up a fight.

The following day, Rei tailed Shinji again. This time, there was no training. Instead, Shinji and the older man walked along the pathway, the teacher passing on his wisdom to the student. Watching from a distance with a pair of binoculars she had 'borrowed' from Section 2, she saw that Shinji was for the first time in his life truly happy.

Rei knew that it was because of the old man.

Which led her to make another decision; should she tell Commander Ikari about this new development?

In the end, she decided to keep her mouth shut. Knowing Gendou, he would try and intimate him into keeping away from Shinji. Or worse. Either way, she still had to make amends for her past behavior, since Shinji was the only person to try and reach out to her.

* * *

Katsuragi Asylum

Rei wasn't the only one concerned for Shinji.

Misato sat at her dining room table, a carton of takeout open, the food untouched, her can of Yesibu unopened. She was alone, since Asuka was spending time at Hikari's house, allowing her some time to think for herself.

Ever since that incident inside the Geofront, Asuka's synch ratio was deteriorating, while Shinji's remained stable. Both her and Ritsuko had originally thought that if had been because of the confrontation between Asuka and Shinji, but Naomi had said otherwise. Shortly before the fight, Naomi had interviewed both Shinji and Asuka (Gendou had refused to let Naomi interview Rei), and the results were in.

While Shinji was suffering from a mild case of post-traumatic stress disorder, Asuka's condition was even more worse. Aside from the inferiority complex, Naomi had labeled Asuka as being a narcissist with a male complex. While Asuka could still pilot, Shinji could not. Despite his solid synch score, he was too much of a risk. So he was temporary removed from the active pilot's roster and placed on the reserve roster, much to Asuka's delight.

Naomi had also warned that Asuka was showing signs of one having antisocial personality disorder. In order words, Asuka was showing symptoms of becoming a sociopath. Despite having plenty of friends and admirers, Asuka was still a sheltered girl, not letting anyone get close to her, with the exception of Kaji and Misato.

Ritsuko, on the other hand, was kicking herself. Despite being the senior medical officer, she had failed to see the signs. Fortunately, Naomi did not bust her ass too bad.

Since Shinji would recognize her in her blue Renault, Misato used an unmarked car to tail Shinji. There, she followed him to the park, where Misato discovered that Shinji had a mentor, someone he could look up to.

It also answered the question about how he was able to defend himself against Asuka.

Whoever he was, Misato noticed that Shinji held him in high regard.

Deciding not to notify Commander Ikari about this development, Misato continued her surveillance. One clue that stood out was his uniform. On the days that Shinji wasn't training with the man, he would walk with the one-eyed man along the pathway, the teacher lecturing the student. He was dressed in the uniform similar to what a senior officer of the JSSDF would wear, save that his was black, identifying him as an officer of the United Nations. And on top of that, he was a general.

After asking around, she had managed to get a name.

John Hayter.

He was a general in the U.S. Army, and had originally retired several years before Second Impact. After the Valentine Treaty had been signed, he was asked to return to active duty, this time as a general of the United Nations, meaning that he easily outranked both Commander Ikari and Deputy Commander Fuyutsuki. Her contact in the JSSDF said that General Hayter is working with the Japanese armed forces as both an instructor and combat analyst.

Misato also found out that he frequently visited a teahouse near the park. The Operations Director decided to pay the old man a visit and ask about her former charge.

* * *

The Geofront, Commander Ikari's Office.

The female undercover agent for Section 2 had done her job well. For the past two days, she had tailed Shinji Ikari, and had acquired surveillance footage of the Third Child training with Big Boss.

Footage that was at the moment being played inside Commander Ikari's office.

Ever since that day in which Shinji had beaten down Asuka, Gendou was becoming very concerned. So he did what was natural to him. He ordered an undercover Section 2 agent to tail his estranged son.

Gendou Ikari watched behind folded hands, along with Deputy Commander Fuyutsuki. The footage had answered the question on how Shinji was able to fight off Asuka. He also appeared to he holding his own against the older man, despite losing the match.

Another video showed Shinji and the old man walking alongside the lake, the pilot of Unit One simply listened with rapt interest, and asking a question once in a while. To make matters worse for Gendou, Shinji was actually smiling. His son was supposed to be in all aspects, a coward who would only fight if ordered to. Now, Gendou could not risk harming Shinji because only Unit One would accept him as a pilot, giving Shinji a major advantage. Without Shinji, Gendou loses Yui.

"Any idea as to who this man is?" Gendou asked.

"I've asked around, and the JSSDF refused to give out his name," the agent replied. "When I told the U.N. that you requested the files, they replied that your clearance is not high enough."

"Hmm..." Gendou looked at the rank on Big Boss's uniform. "He is a General in the American branch of the U.N. Forces. Anything else?"

"He is working as a combat instructor with the JSSDF," the woman replied. "That was all I was able to find out about him. His background is classified by the American government and the U.N."

With a wave of his gloved hand, Gendou dismissed the security agent.

"So he is protected," Fuyutsuki said.

"That he is," Gendou admitted. He was expecting a low-level peon which he could threaten and intimidate. Instead, he found a high-ranking officer – a guest of the Japanese government – tutoring Shinji in the art of combat. "It would also explain how the Third Child was able to defend himself against the Second Child. This...general is a threat to the scenario."

Fuyutsuki did not like where this was going.

"Professor, I want his dossier on my desk in one hour," Gendou demanded. "I want to know exactly what we're dealing with here. Have Dr. Akagi use the MAGI if necessary. I want to know everything."

Fuyutsuki nodded and exited the room.

* * *

Inside the teahouse, Big Boss had long since noticed the blue Renault outside. Both Shinji and Kaji had verified that only Misato drove the Alpine, and the old soldier quickly deduced that Major Katsuragi was coming to speak to him about Shinji.

From what Kaji had told him about his old flame, she was the Tactical Operations Director of Nerv, as well as the sole survivor of the Katsuragi Expedition. Big Boss had his concerns about the woman, but Kaji had vouched for her, saying that if there was one person that he could trust, then it would be her.

Misato stepped inside, she looked around for a moment, before spotting him in a corner booth, reading over some documents. He didn't appear to notice her, as he was into his work.

Misato walked over to his booth. "Excuse me? General Hayter?"

Big Boss looked up from his documents, sizing up the young major with his eye, causing the woman to squirm under his gaze. "You just as how young Ikari described you, Major Katsuragi." Off Misato's surprised look, Big Boss continued. "Yes, he's told me quite a bit about you. I take it you are here regarding him, correct?"

Misato nodded. "Yes, General."

"Please have a seat," Big Boss said, gesturing to the seat across from him with one gloved hand.

Misato sat down. One of the waitresses appeared and set down a cup of warm tea in front of the legendary soldier. Misato declined to order some tea for herself when asked by the waitress.

"You are sure?" Big Boss asked, taking a sip of the tea. "The tea here is very good."

"I am sure," Misato replied politely. "As you already know, I am here in regards to Shinji. I just want to know why. Why take such an interest in him? Because of you...he's changed. I can hardly recognize him anymore. Part of that hatred is directed at his father and most of the Nerv staff...but now...I just want answers, General."

Big Boss leaned back in his seat, arms folded across his chest. "Have you ever really sat down and talked to the boy? See how he truly feels about piloting the Evangelion, Major? Of course not. So long as the Angels are destroyed, who really cares how the pilot think, right? Underneath all of that self-doubt, there is nothing but rage. Rage towards his father for forcing him to pilot."

Misato remembered that day well. Gendou had ordered Shinji to pilot once he was brought to the EVA Cages. When Shinji refused, Gendou had brought out an injured Rei, threatening to use her as a pilot in his place.

"Have you ever seen a child soldier snap under stress?" Big Boss asked. When Misato shook her head no, Big Boss continued. "Children who suffer from post-traumatic stress disorder are most likely to lash out, in most cases violently. I met Shinji shortly after the Angel had assaulted the Geofront. Oh, yes. I know. Shinji told me everything. Even if he didn't tell me, I would eventually find out, given that my clearance is much higher than yours, Fuyutsuki's and Ikari's. Despite saving the city countless times from the Angels, he feels unappreciated, betrayed and used. Instead of a 'thank you,' or a pat on the back, he is given nothing but contempt."

"Shinji would have said something," Misato pointed out.

"But would you have listened to him?" Big Boss replied.

"I..." Misato's comment died on her tongue.

"Did you know that Shinji was going to kill himself?"

Misato's eyes widened at that little revelation.

"I met him at the park. He had a pistol in his hand and had planned on blowing his brains out. But I stopped him. He said that he stolen the gun from your room."

'So that's what had happened to my gun,' Misato thought.

"His original intention was to gun down both Sohryuu and Ayanami before killing himself, but went against it," Big Boss continued. "Reaching out to him was the last thing I had expected to do, but he reminded me of a young boy I rescued many years ago."

He leaned back into his seat. "Ironically, he also reminds me of myself. Let me tell you a story, Major."

[Here, the scene fades, and we go into a series of flashbacks, this time, from Big Boss' mission into Russia fifty years earlier.]

BIG BOSS: (voice-over) Fifty years ago, I was sent into Russia to retrieve a man named Nikolai Stephanovitch Sokolov, a high-ranking weapons developer who was defecting to the West. Most people don't know this, but I was the first person in history to ever perform a HALO (High-Altitude, Low-Opening) jump into the former Soviet Union. That was a pretty amazing rush for me. But back to the story at hand.

[Shot of the younger Big Boss, holding the Knife and his Pistol.]

NAKED SNAKE: Commencing Virtuous Mission...now.

[Shots of The Boss, Colonel Volgin and the Cobra Unit. We see The Boss beating the crap out of Big Boss, er...Naked Snake on the bridge, right before tossing him into the river. Next shot is that of Volgin using the Davy Crockett to nuke Sokolov's facility.]

BIG BOSS: (voice-over) That mission was a failure due to someone close to me betraying me and leaving me for dead. Even worse, the U.S. was framed for the destruction of Sokolov's facility. Because of what my mentor had done, I was accused of being a traitor, as was the members of my old unit.

[Next shot is that of Naked Snake executing Operation Snake Eater. He is taking down each member of the Cobra Unit; The Pain, The Fear, The End, and the Fury. Next shot is that of Volgin being fried by a bolt of lightning on top of the Shagohod.]

BIG BOSS: (voice-over) I later returned and not only eliminated her former unit, but also the renegade Soviet colonel that was her host. It was also the same time I got this memento. (gestures to the eyepatch)

[Shots of the confrontation between Snake and The Boss at Rokovoj Bereg.]

BIG BOSS: (voice-over) I faced my mentor in combat. Even after five decades, I still remember her words to me.

[Shot of the Boss.]

THE BOSS: The one who survives will inherit the title of Boss. And the one who inherits the title of Boss will face an existence of endless battle.

[Shot of the climatic battle between The Boss and Naked Snake. Snake defeats The Boss.]

BIG BOSS: (voice-over) It was the longest ten minutes of my life. But I accomplished my mission I defeated The Boss.

[The Boss hands Snake The Patriot.]

NAKED SNAKE: A Patriot?

THE BOSS: Jack...or should I say...Snake...You're a wonderful man. Kill me. Kill me now. Do it. There's only room for one Boss...and one Snake...

[Snake executes The Boss. Next shot is that of Snake inside the lodge, listening to EVA's confession on the tape player.]

BIG BOSS: (voice-over) I honored her last request. I killed her. It was only in the aftermath that the truth was revealed to me. Her defection to the Soviets was all but a ruse set up by the American government in order to gain the upper-hand on the Soviets. But the mission parameters had changed. In order to prove to the Soviets that the Americans were innocent, I had to kill my mentor.

EVA: (from the recording) Snake, history will never know what she did. No one will ever learn the truth. Her story...her debriefing...will endure only in your heart. Everything she did, she did for her country. She sacrificed her life and her honor for her native land. She was a real hero.

[Final shot is that of the newly-christened Big Boss saluting her grave.]

EVA: (from the recording) She was a true patriot.

[Back to the present...]

Misato sat there, eyes wide as Big Boss finished his story.

"Killing The Boss has left me empty, even to this day," Big Boss continued as he fondly remembered the days when he was her student. "So I took solace in the battlefields. I never could let it go. The Boss was something of a spiritual mother to me. She taught me how to fight, how to fire a weapon, damn near everything I know." He sighed. "I have...three sons. Well, make that one, since two of them died after the Impact. I can honestly say that the remaining one and I were at odds in the past, but we made our peace."

He paused for a moment to down the remainder of his tea. "I listened to Ikari as he told me his story. It's a miracle in itself that he did not snap under the strain of being a pilot. Scientists should never be allowed to conduct military operations. They are not soldiers. They make rash decisions in which can have catastrophic results. He wanted to become more confident, more assertive. So yes, to answer your unspoken question, I took him in as my student in CQC."

"CQC? Close-quarters-combat?"

"He said that he was tired of being afraid, tired of running away from his problems. I can safely say that despite being the first person I taught since the Impact, Shinji is very talented. He also told me about the confrontation with the Red Devil."

"Red Devil?" Misato repeated. She then realized who Big Boss was referring to. "You mean Asuka."

The old man nodded, as a waitress handed him a refill of tea. "Yes. I can see why Shinji despises her. The girl clearly has some personal issues she needs to deal with, as well as an inferiority complex. Things like that could get her killed, as well as everyone else. In war, you never fight for glory. You fight solely to survive. Sohryuu is fighting solely for the former, which makes her a serious liability."

Misato knew that Big Boss was right. It had taken Shinji moving out to see that Asuka was starting to get out of control. That lack of control was in fact, a major liability in Nerv. It was only the restraining order Shinji had placed on Asuka as well as the threat of being fired from Nerv that made Asuka fall back in line, if only temporarily.

Big Boss looked at the woman for a moment. "Katsuragi...you're related to Doctor Hideaki Katsuragi?" he asked.

Misato nodded. "He was my father, General."

"So that means you were actually there when Second Impact took place," Big Boss surmised. "You do have a soldier's spirit within you, if you managed to survive that hell."

"I only survived because of my father," Misato replied. "He placed me inside an escape capsule." She gestured to the cross around her neck. "This was also his. I guess he knew that he was going to die, and he wanted me to live."

"You never got along with your father, didn't you?"

Misato shook her head. "No. Total workaholic. Yet...when Second Impact struck...he saved my life."

"A parent's first responsibility is that to his children," Big Boss explained. "Never forget that, although my relationships with my sons have been less than peachy. Your father wanted you to live."

Before Misato could reply, the alarms began to ring. Outside, the people scampered to the shelters. Misato's phone began to ring. She quickly retrieved it from her jacket pocket and answered. "Katsuragi."

"Major, we got a blue wavelength," Hyuuga's voice replied from the other end.

"I'm on my way," Misato replied. Hanging up the phone, she turned to Big Boss. "Sorry, sir. But I'm needed. Get to a shelter. And thank you for your time."

Big Boss nodded. "Not a problem. One more thing, Major."

Misato turned around. "Sir?"

"Watch yourself around Commander Ikari," Big Boss warned. "He is not someone to be trusted. The man has an ulterior motive."

Misato quickly left the teahouse. Big Boss rose from his seat and walked outside, where a parked sedan waited. He got into the back seat, closing the door behind him.

In the seat next to him, was Ocelot.

"It's time," Big Boss said calmly. "Is everything ready?"

"RAY 3 is prepared to sortie," Ocelot replied.

To the driver, Big Boss ordered, "Mount Futagoyama."

"Yes, sir," the driver replied before peeling off.

* * *

The Geofront - ten minutes later...

The images from the orbital satellite were in. Sure enough, in a low-earth-orbit, was Angel number fifteen.

Arael.

To Misato and Ritsuko, it looked like a freakish, glowing multi-winged bird of light.

With the exception of Shinji, both Asuka and Rei were already in their EVAs. Shinji, on the other hand, was standing beside Naomi. On her recommendation, Naomi had requested that Shinji should sit this battle out, pending his PTSD treatment. Gendou and Fuyutsuki had agreed.

"We have visual confirmation," Hyuuga said. "It's an Angel. Satellite's at maximum zoom. So far, it has not moved from its position."

"Which makes it impossible for us to attack it," Aoba added.

"What is that Angel planning to do?" Misato pondered. "Is it just going to sit there, or is it going to destroy us from its position?"

"At this rate, we can't attack it. It's too far out in LEO," Hyuuga pointed out.

"Smart move, staying out of our firing range," Misato concluded. "How is Rei and Unit Zero?"

"Both are in good position and ready to move out," Maya replied.

"Good," Misato nodded. "Equip Unit Zero for long-range firing and launch."

* * *

On the launch pad, Asuka Sohryuu was inside her EVA. Originally, she felt giddy that Shinji was ordered to sit out this battle. Wondergirl to her wasn't that big of a threat, meaning that she would kill the Angel and take the credit for herself.

That is, until Misato's image appeared on screen and issued the battle orders.

"Asuka, you are to back up Unit Zero," Misato ordered.

"What? Back Wondergirl up? Forget it!" Asuka objected.

"You have your orders, Pilot Sohryuu!" Misato snapped. "You're the rear guard."

"You can't be serious!" Asuka shouted. "EVA Unit Two, launch!"

'Now why am I not surprised?' Misato thought as she watched Unit Two rocket towards the city surface. In the back of her mind, Big Boss' words came back to her.

'Things like that could get her killed, as well as everyone else. In war, you never fight for glory. You fight solely to survive. Sohryuu is fighting solely for the former, which makes her a serious liability.'

Deep down, she hoped and prayed that Asuka's recklessness did not get her killed.

* * *

Meanwhile, at Mount Futagoyama...

Located on the outskirts of Tokyo-3, Mount Futagoyama was the location of the Yashima Operation several months before, where Shinji had sniped Ramiel. Now, the mountain itself was deserted, the remains of various pieces of equipment still there, as the JSSDF did not have the time nor the manpower to remove the equipment from the mountain.

Up in the sky, a dim blue light was seen. Arael has arrived. The Angel of Birds kept its distance, far out of reach of conventional weapons.

Big Boss stood outside of the makeshift operations center, looking out at the city below, a lit cigar in between his lips. The umbrella he gripped in his hand shielded him from the rain.

'EVA always did enjoy the rain,' the old soldier thought as he fondly thought of his lover, taking a puff of his cigar, blowing the smoke out. 'Then again, so did I.'

Big Boss could not deny that he had plenty of good times with the former Chinese spy. Even back when they were part of Zero's Patriots, they always made time for each other. After losing to Solid Snake in Outer Heaven, it was EVA who had taken him to Japan to recover from their epic duel.

It was also EVA that had convinced him to make his peace with Solid Snake before it was too late.

"A penny for your thoughts?" Ocelot asked as he stepped outside, an umbrella in his own hand.

Big Boss' eye looked distant. "She always enjoyed the rain," he said, still looking out into the rainy night sky.

Of course Ocelot knew who he was talking about. Unlike Big Boss, Ocelot saw EVA as something of a elder sister. Her death had hit Big Boss as hard as The Boss' death had 50 years earlier. Only difference was that Big Boss was his mother's executioner.

Ocelot did not find out about the truth regarding his parents until shortly after Big Boss was recruited into the Patriots. How his mother had given birth to him in the middle of the Normandy invasion. How his mother had killed his father, The Sorrow. And of how Big Boss had honored his mother's final wish of defeating her in combat. Even after all this time, Ocelot held no ill will towards the older man for the events of Operation Snake Eater.

"EVA was my friend as well," Ocelot said. He looked at his watch. "It's time. Nerv will be releasing their Evangelions to fight Arael. RAY 3 should be moving into place soon."

"And the ion cannon? Will it have enough power to destroy the Angel in orbit?" Big Boss asked.

"It's Patriots technology at its finest. Something that Nerv does not have. All RAY has to do is compute a firing solution, and it will do the rest."

"Excellent," Big Boss replied as he turned around and entered the operations center. Aside from Kaji and the techs on the Patriots' payroll, three generals were present. As it turned out, they were the same three JSSDF generals who were there at the Geofront when Sachiel had attacked.

The three men were also veterans of Outer Heaven and Militares Sans Frontières, and fiercely loyal to Big Boss. It was through Big Boss that they had gotten officers' commissions with the JSSDF upon its formation years earlier.

The three men rose from their seats and bowed. "Big Boss, sir!" the three men barked.

"As you were," Big Boss said. "Status report."

"RAY 3 is moving into position," the senior tech reported. "Stealth camo is working at 100 percent."

"Prepare to fire," Ocelot ordered.

The tech nodded and moved to perform her duty.

"You do know that once the cannon reaches maximum power, we lose the stealth camo," Ocelot noted. "As advanced the tech is, it still needs to be tweaked."

"I know."

"And what if Unit Two attacks RAY?" Ocelot asked his former mentor.

"Simple. We use the water cutter to knock it on its ass. If it becomes too stubborn, then we destroy the core." Turning to the JSSDF personnel, he said, "Begin the operation."

The silent RAY slowly moved into its firing position, stopping once it was behind Asuka's Unit Two. Its maw silently opened, and the cannon slowly began to power up. It would take at least ninety seconds before it would reach full power.

* * *

Inside Nerv Headquarters, Shinji watched Unit Two on the monitors along with Naomi and the rest of the senior Nerv hierarchy. Unit One was going to be down for quite sometime. Aside from the fact that Naomi had diagnosed Shinji with PTSD, he would be sitting this battle out.

Which suited him just fine.

It was at that moment, Aoba noticed something...odd on the monitor. It was still raining, so why was the rain behind Asuka was bouncing off of something...very, very big?

Misato noticed it as well. 'What the...?'

It was at that moment, the stealth camo failed and RAY 3 was revealed in all its glory, preparing to fire.

"Asuka, behind you!" Misato shouted.

* * *

"Asuka, behind you!"

"Huh? Wha...?"

Asuka spun around, and found herself facing an unknown mecha about the size of an Evangelion.

And from the look of things, it was preparing to fire on her. And from this range, now even her AT-field would not stop it.

"Oh...SHIT!" Asuka cursed as she dove out of the way...

...just as Arael's beam of pure light struck the spot where Asuka's EVA had been standing at moments earlier. Arael then quickly brought its beam on the RAY, bathing it in its attack.

Unlike the EVAs, RAY was completely unmanned, controlled by a AI, just as Arael would soon find out.

* * *

On Mount Futagoyama, Big Boss and Ocelot watched as Arael tried to probe into RAY, but with no success.

"Cannon charge is 100 percent complete," the senior tech reported. "We got a firing solution on the Angel."

"Fire," Big Boss ordered.

* * *

RAY 3 fired.

Not as Asuka, but upwards. The ionized particle beam shot upwards at the speed of Mach 4. Arael brought up its AT-barrier to full power in order to deflect the beam, but it was a fraction of a second too late. The ion beam destroyed the core, and with it, Arael.

* * *

Nerv Headquarters.

Silence reigned throughout the bridge as to what had just transpired. The mechanized monstrosity had all but destroyed the Angel in one move. Even Gendou was shocked at this new development.

"The...the Angel is gone!" Maya gasped. "There is no trace of it!"

"What the hell was that?" Misato demanded, turning to Ritsuko.

"I don't know," the blonde replied, still shocked at how the new mecha had destroyed the Angel without little effort. "Maya?"

"Scanning the mecha through the MAGI, Sempai," Maya replied. "The MAGI does not recognize the mecha."

The gears in Misato's head were starting to turn. 'If that mystery mecha could destroy an Angel in one blast, then what kind of damage could it do to an EVA? This is not good,' Misato thought.

"Asuka, return to base now," she ordered. "We have no idea as to what that mecha is. I repeat, return to base."

"Belay that order."

Misato and Ritsuko turned around. Gendou was on his feet. And he did not look very happy at this development (big surprise!).

"Pilot Sohryuu, you will disregard Major Katsuragi's previous order. I want that mecha. Do you hear me? Capture that mecha," Gendou ordered. "Use whatever means at your disposal."

"Then send me a damn rifle!" Asuka shouted.

* * *

Mount Futagoyama.

_"Pilot Sohryuu, you will disregard Major Katsuragi's previous order. I want that mecha. Do you hear me? Capture that mecha. Use whatever means at your disposal."_

_"Then send me a damn rifle!"_

Of course, Big Boss and Ocelot knew what was going on. After all, it was easy to hack into the MAGI, giving the Patriots a back door into Nerv. And the JSSDF had some of the best hackers on their payroll, allowing The Patriots to use their talents to get inside of Nerv, from their phone lines to their video feeds inside the Evangelions.

Ocelot and Big Boss exchanged looks. "This is why scientists should never be in charge of military operations," the Patriots chieftain mused as he watched Unit Two retrieve two palette rifles from the weapons locker. "Especially Gendou Ikari."

Thanks to the hackers, Big Boss had been reading up on the Supreme Commander of Nerv. As it turned out, the estranged father of Shinji Ikari had plenty of skeletons in his closet.

More importantly, he was the one who had sabotaged the Contact Experiment with ADAM, thus triggering Second Impact, on Seele's orders. The original intention of the Contact Experiment was to conduct research on ADAM's S² Core, but Gendou had tampered with the experiment, thus unleashing the hell that was Second Impact.

And now, Gendou was preparing to unleash his own version of Third Impact in an attempt to reunite with his wife, who was inside Unit One. Even if it means killing his own son and the rest of the world in the progress. And given what happened on Second Impact, Ikari was not squeamish on ending human lives, even on Seele's orders.

Ocelot wanted to kill him upon finding out that Gendou was the one responsible for the Impact, but Big Boss refused.

"In due time, Shalashaka," Big Boss had said. "In time, in our own special way...Ikari will answer for his crimes."

From RAY 3's optical sensors, which gave them a video feed to the facility on Futagoyama, Big Boss, Ocelot and the JSSDF personnel watched as Asuka retrieved two palette rifles from a weapons rack which had risen from the ground.

"Your orders?" Ocelot asked.

"No need to ask," Big Boss replied. "I believe Sohryuu is looking for a fight. Humor her. But don't kill her."

Ocelot grinned evilly. "With pleasure." Turning to the techs, he said only one word. "Sortie."

* * *

Back in Tokyo-3, the rain had picked up as RAY 3 made its challenge known in the form of its trademark scream. Armed with two palette rifles, Asuka opened fire with both of them, the spent shells falling to the streets, some of them destroying parked cars, if Unit Two had not already crushed them underfoot as the red EVA charged.

The rounds from the palette rifle harmlessly bounced off RAY 3's armor.

Asuka dropped the empty rifles and went for her Prog Knife.

Which did absolutely no good when RAY 3 body-checked Unit Two with brutal force, sending the red production-model EVA to the ground, Asuka losing her grip on the Prog Knife, which as she watched, was crushed under the RAY's heel. While Asuka forced Unit Two to its feet, RAY's missile silos opened on its back, and the Metal Gear launched a volley of rockets at Unit Two.

Asuka's reaction was instant. Her AT-Field was up, and the missiles detonated against the field. However, it had obscured her vision. When the smoke had cleared, RAY 3 was gone.

Asuka looked around. "Where are you?" she shouted.

After a moment, it appeared that RAY 3 had retreated. Of course, Asuka, being Asuka, reacted automatically. "Whatever it was, it ran off. Coward. Just like Baka-Shinji! I told all of you that I'm the best! That reject has ran off like a coward instead of facing the great Asuka Langley Sohryuu!"

It was at that moment, that RAY 3 had appeared, using the smoke from the rockets to trigger its stealth camouflage, and thus outflanking Asuka.

"ASUKA, WATCH OUT!" Misato screamed.

Too late.

RAY 3 fired off one single rocket, nailing Unit Two in the back. Not only it caused major damage, it also had the effect of destroying Unit Two's power cable, reducing the red EVA to battery power.

Meaning, it had less than three minutes to either escape or fight.

"Damn!" Misato cursed. "That thing has some kind of stealth technology! Asuka, withdraw!"

Once again, Misato was overruled by Gendou. "Belay that order," he barked. "I want that mecha!"

"Commander, she can't win!" Misato appealed. "She only has two minutes of battery time left. She has to retreat!"

Gendou leveled his gaze on Misato. "Major Katsuragi, one more word out of you, and I will have you arrested for gross insubordination."

Misato growled internally. Gendou was more than willing to sacrifice Asuka to capture that mecha, and she was helpless to do anything. Shinji just watched the brawl with great interest, while at the same time, not surprised at his ex-father's veiled threat. So far, all of Asuka's training wasn't worth shit, since she now had one minute of power left.

Naomi, on the other hand, knew what the RAYs were capable of.

Back on the surface, Asuka looked at her timer. Forty-five seconds left. Her ego had all but overridden her common sense, the latter telling her to retreat.

And she paid for it.

The water cutter from RAY 3 was something Asuka was not expecting. The blast had all but knocked Asuka to the ground, just as her internal battery had ran out of power.

RAY 3 let out a screech before pouncing on top of the downed EVA.

This fight was over.

Then Unit Zero appeared, armed with a Mag-Rifle. Unit Zero opened fire on RAY, who simply jumped off of Unit Zero, and returned fire, firing short bursts from its ion cannon.

Rei brought up Unit Zero's AT-Field, but found out that it was no use, as the particle beams had penetrated through the field, striking Unit Zero in the shoulder, damaging it, as well as its knee, causing it to stumble.

Now behind Unit Zero, RAY 3 severed the EVA's cable, before punting it away, causing it to land on a undignified heap on top of Unit Two. Letting out a triumphant roar, RAY 3 made its exit, bounding over buildings before reaching the beach, where it leapt into the ocean with a huge splash.

"Damn it!" Gendou cursed, slamming one gloved fist onto the console. His chance of obtaining that mecha had all but failed.

"Get the recovery teams to Units Zero and Two," Misato ordered. "And find out what the hell was that thing that destroyed the Angel!"

Shinji, in the meantime, slipped out of the bridge, and made his exit from the Geofront.

* * *

Mount Futagoyama.

"That was fun," Ocelot had said once RAY 3 was safely away from Tokyo-3. The massive RAY was heading back to its fallback spot in southern Japan.

"Indeed," Big Boss replied. Turning to the JSSDF staff, he addressed them. "Good work, from all of you. The battle has been won, but we have one more Angel to deal with. All of you are dismissed."

* * *

The Geofront, an hour later.

"So how bad is it?" Misato asked as she, Naomi, and Ritsuko stood in the EVA Cages, looking over the battered Unit Two.

"Pretty bad," Ritsuko replied. "We may have to take Unit Two down for the repairs. The most prominent of the damage is the destroyed power socket and core. The damage to Unit Zero is minimal. But it's going to be a while before Unit Two is combat-ready again. First, we need to repair the core."

"Any ideas as to what destroyed the Angel?" Misato asked.

"None whatsoever," the Project E chairwoman replied. "It's technology is radically advanced. A particle cannon capable of penetrating AT-Fields. And that stealth technology...the Commander is not very happy at the moment."

"Because whatever that mecha was has all but made a fool out of all of us," Misato guessed. "Especially Asuka."

Ritsuko winced in sympathy. "And you're her guardian as well. I feel for you. I could hear her as we got her Entry Plug out, blaming Shinji for the entire thing."

"Sohryuu is becoming a liability," Naomi said. "Her synch ratio has been declining since Ikari's return from Unit One."

"Maybe he was right," Misato sighed.

"Who?"

"I found Shinji's mystery mentor," Misato explained. "He's a general in the U.N. Pretty old-school too. Name's Hayter."

'That should make the search a lot easier,' Ritsuko thought. Shortly before the Angel attack, Gendou had ordered her to use the MAGI to discover the identity of Shinji's mentor. Now, Misato had inadvertently given her a vital clue.

Misato shook her head. "This whole battle was nothing more than a mess. Asuka should have retreated."

It was at that moment, she remembered something that Big Boss had told her hours earlier.

_'Scientists should never be allowed to conduct military operations. They are not soldiers. They make rash decisions in which can have catastrophic results.'_

Misato realized that he was right. Gendou had overrode her authority as the Operations Director because of his desire to obtain the unknown mecha. Now, Unit Two was badly damaged and was in danger of losing the core. Without the core, then EVA Unit Two would be dead weight.

And if that happens, then that may push Asuka off the deep end.

Little does Misato or anyone else know, that Asuka Sohryuu - blinded by her own ego and desire to be the best - was already on her path to self-destruction.

* * *

Commander Ikari's office, some time later...

"Well?" Gendou demanded as Fuyutsuki entered his office, followed by Ritsuko.

Thanks to Misato, Ritsuko had accomplished her task. She had found Big Boss' dossier. Unknown to her, it was a slightly modified version of Big Boss' dossier, since Big Boss had correctly guessed that Commander Ikari would come sniffing around, trying to find out who he was once it became known that he was mentoring Shinji.

The erstwhile lover of Gendou Ikari placed the dossier on the desk. "It appears that the Third Child has quite the mentor," Ritsuko noted as Gendou leafed through the dossier. "General Hayter has quite the military history."

"Hmm...Jackson David Hayter," Gendou read. "Born 11 July 1935. 192 centimeters tall. Served with the U.S. Army's Green Berets and later the Army Rangers. Worked for the CIA as an operative of the now-defunct FOX unit. Also worked with LRRP (Long-Range Reconnaissance Patrols) and SOG (Studies and Observations Group) during the Vietnam War. Worked as a mercenary for a time...The Wild Geese and founded Militares Sans Frontières Was called back to active duty following Second Impact. Currently a five-star general, working with the JSSDF as a combat analyst and trainer. Over five hundred missions and operations in his career before the Impact."

Gendou closed the folder as he took in the information. His son was dealing with a career soldier. A battle-hardened career soldier whose clearance and authority easily dwarfed his own.

But Gendou would not be denied. He had waited for so long to get Yui back. Not even his son nor his mentor, or even Seele would stand in his way.

"Ikari, this is a dangerous game you are playing," Fuyutsuki warned. "This is a high-ranking officer of the United Nations we are dealing with. One that the Third Child has taken quite an interest with."

"That is irrelevant," Gendou replied icily. "General Hayter is a threat to my scenario. Have Section 2 scour the city for this man. Once they find him, bring the General in. I wish to speak with him personally."

"Understood," Fuyutsuki said, both he and Ritsuko leaving the room.


	6. Episode 5: Bitter Truths

_**Episode 5: Bitter Truths**_

Snafu's Notes: The story's halfway finished. Also, to answer some of the private messages I've been receiving, The Wild Geese is a mercenary unit Big Boss worked with, not the group of the same name from Hellsing. Also, this chapter's pretty long. Oh, and reread Episode 3, as I've added the Beauty and Beasts Unit to the story. Also, there is a twist that you will see coming.

Commander Ikari's office, shortly after the battle with Arael.

"Ikari, this is a dangerous game you are playing," Fuyutsuki warned. "This is a high-ranking officer of the United Nations we are dealing with. One that the Third Child has taken quite an interest with."

"That is irrelevant," Gendou replied icily. "General Hayter is a threat to my scenario. Have Section 2 scour the city for this man. Once they find him, bring the General in. I wish to speak with him personally."

"Understood," Fuyutsuki said, both he and Ritsuko leaving the room.

'Ikari has no idea who he is dealing with,' the aged Deputy Commander thought as he headed for his own office. 'Against someone like Big Boss, he is outclassed.'

Kouzou Fuyutsuki had good reason to fear Big Boss more than his pupil. He had met the man personally. Shortly before Arael's attack, he had been kidnapped by Seele and interrogated. It was only through Kaji that he was able to escape. Of course, Seele had found out and their judgment was swift: termination.

However, Ryouji Kaji would not die that day.

* * *

[Flashback - two days before Arael...]

Kaji watched as five armed men entered his hideout. "You found me at last. I've been expecting you. My friends really wanted to meet you."

From the shadows in the far corner, gunfire erupted. Four of the gunmen went down, dead before they hit the floor. One of them got a wound to the shoulder and leg.

Big Boss and Ocelot stepped out of the shadows, the former placing his M1911 pistol on safety, while the latter casually twirled a smoking Colt revolver.

"Good grouping," Kaji noted. He looked at the surviving assassin. "We got a live one here."

Ocelot holstered his gun. "He's mine."

Ocelot once said that torture was the 'ultimate form of expression.' This was during Operation Snake Eater, when Big Boss himself was tortured at the hands of Colonel Volgin. Ocelot wasn't nicknamed Shalashaka for nothing. Of course, Kaji did not have the stomach to watch the 'interrogation,' in which he excused himself from the proceedings.

After several minutes of Big Boss, Ocelot and the other man speaking in German, a gunshot was heard, signaling the gunman's demise. Seconds later, Kaji was summoned back inside.

"I love interrogating hit men," Ocelot said, looking at the dead hit man. "No matter what they do, I really don't feel bad."

"So...what did you find out?" Kaji asked, trying to keep his stomach under control.

"As we both expected," Ocelot replied, "the hit men in question were in fact from Seele. We also found out that Seele will move forward with their plan to wrest control of Third Impact from Commander Ikari. It also appears that they do not entirely trust the U.N., or the JSSDF."

"It gets worse," Big Boss continued. "Seele's hired Haven Troopers to launch a no-survivor assault on the Geofront, should they fail to get the JSSDF to attack."

"Looks like we'll have to call in Snake and the others in sooner than expected," Big Boss said.

Ocelot nodded. "I'll summon them to Tokyo-3 immediately. Do we have a time table?"

"Probably less than a week after the last Angel." Big Boss walked up a nearby flight of stairs, walked down the hall, and into a back room. "First things first."

There, seated in a chair, was a bound Kouzou Fuyutsuki. He was blindfolded, his mouth taped shut.

Big Boss pulled up a chair and sat down, while Kaji moved behind the bound old man. "Deputy Commander Kouzou Fuyutsuki, of the U.N. anti-Angel organization Nerv. Can you hear me?"

Fuyutsuki nodded.

"Good. Ocelot?"

**CLICK.**

Fuyutsuki heard the unmistakable sound of a hammer being pulled back.

"Did that get your attention?" Big Boss asked. When Fuyutsuki nodded, Big Boss continued speaking. "At the moment, my associate has a gun aimed at you. During this time, I will have your bonds released. If you try to run, or attack any of us, you will be dead before you hit the ground. Understood?"

Again, Fuyutsuki nodded.

"Good," Big Boss replied. "Mr. Kaji?"

Fuyutsuki felt his arms freed. Then he could see, as the blindfold was removed. Sure enough, the one-eyed old man was seated in front of him, while the other old man with the long hair had a revolver aimed from the hip.

"I heard that if you rip the tape off fast, it won't hurt as much," Ocelot suggested.

Kaji shrugged his shoulders. "Worth a shot," he said, right before yanking the tape off of Fuyutsuki's mouth, making the old Deputy Commander whimper.

"So much for that theory," Ocelot had said, chuckling.

"I believe that introductions are in order," Big Boss said. He gestured to Ocelot. "The man with the Colt revolvers is Revolver Ocelot." He nodded to Kaji. "You already know Mr. Kaji. You can call me Big Boss."

Fuyutsuki swallowed audibly.

"I know this wasn't something that you were expecting," Big Boss continued, playing the diplomatic role. "First being kidnapped and interrogated by Seele, and now kidnapped by us. But I have some questions for you, Professor. Given your position within Nerv as second-in-command, I feel that you can

help. If you cooperate and answer my questions truthfully, then I give you my word that you will be released unharmed. However, if you jerk me around, I'll let Ocelot question you. Are we clear?"

"Yes," Fuyutsuki replied. He had clearly heard Ocelot's 'interrogation' downstairs.

"You come from a respectable background," Big Boss noted. Off Fuyutsuki's surprised expression, Big Boss continued. "Your parents were survivors of the Hiroshima bomb, and prior to Second Impact, you were a professor of metaphysical biology at Kyoto University. Yet, you align yourself with Seele. Why?"

"There's an old saying," Fuyutsuki replied. "'Sometimes, it's better to be the right hand of the Devil, rather than in his path.' When I found out about the truth behind Second Impact, I confronted Gendou about it, threatening to expose him and Seele. Gendou countered with a choice: join Gerhim and work for him or die."

"With the exception of Major Katsuragi and maybe Doctor Akagi, you are an innocent...yet you stood by and did nothing," Big Boss stated. "Why didn't you tell someone about Second Impact?"

"Seele...they control the U.N.," Fuyutsuki said. "They control Nerv."

"We know that Ikari was responsible for Second Impact," Ocelot said. "What is his stake in Third Impact?"

"Ikari...Gendou wishes to control Third Impact in order to ascend into godhood in order to reunite with his wife."

"Explain," Big Boss ordered.

"Ten years ago...Yui Ikari conducted a Contact Experiment with Evangelion Unit One," Fuyutsuki explained. "Her body was reduced to LCL as a result of reaching a 400 percent synch ratio, her soul absorbed into Unit One."

Of course Big Boss and Ocelot knew about the Evangelions. Aside from Shinji, Kaji was vital in explaining how the Evangelions worked. And soon, the hackers working for the JSSDF would have a back door into Nerv by hacking into the MAGI.

"Gendou believes that by using the forbidden union of ADAM and Lilith, he can bring Yui back from Unit One's core...at the cost of every living being on this planet."

"That's something we cannot allow," Big Boss said. "Seele and Ikari must be stopped."

Fuyutsuki chuckled bitterly. "How? You can't stop them. Ikari, maybe, but Seele is untouchable. They also have their own plans for Third Impact."

"I doubt that," Ocelot replied. "Have you heard about the Tarumae Incident?" When Fuyutsuki nodded, Ocelot continued. "There was a hidden Seele facility there. The facility housed the mass-produced EVAs that Seele intended to use for Third Impact, as well as the final Angel, Tabris. That facility, along with the EVAs and the last Angel, have been wiped out. Amazing what you can do with a Metal Gear and a N² mine."

Fuyutsuki slowly digested this new information. The mass-produced EVAs were destroyed, along with Tabris. Was Seele keeping this piece of information away from Gendou for a reason?

"Without the mass-produced EVAs," Big Boss cut in, "Seele has no other choice but to invade the Geofront and to seize control of Third Impact from Gendou. But Ikari himself is a serious threat. He has ADAM in his possession, as well as Lilith in Terminal Dogma. If I were a betting man, Ikari will make his move once he finds out that there is no Tabris."

"That would be the most feasible conclusion," Fuyutsuki noted, still wary of Big Boss and Ocelot, the latter still having his gun drawn and aimed at him. But even Fuyutsuki had to admit that despite his subordinate having a gun aimed at his head, Big Boss was cordial, even respectful towards him, unlike Seele, which slightly put him at ease.

"For now, your life is yours still," Big Boss said. "However, if you mention this little meeting to Commander Ikari or anyone else, then your life is forfeit."

Fuyutsuki knew that the older man was dead serious. He gulped audibly.

"I have spies and informants inside Nerv. They will be watching very closely," Big Boss warned. Turning to Kaji, he said, "Return him to the Geofront."

Kaji nodded. "Sir." To Fuyutsuki, he said, "Come on, Deputy Commander."

Once Kaji and his 'guest' were gone, Ocelot turned to Big Boss. "I think I'll contact Snake now."

Big Boss nodded. "See to it."

[End Flashback]

Fuyutsuki slumped deeper into his chair. 'Gendou has no idea as to what is happening,' he thought. 'If he knew that his scenario was destroyed, he would be livid.'

* * *

The following day, after Arael's attack...

Today was Big Boss' day off.

Rarely, the old man took some time for himself, but today the old man made an exception, and for good reason. Today was the second anniversary of Seele's attack on the Patriots. That results of the attack were the deaths of EVA and Roy Campbell. Earlier that day, both him and Ocelot had drunk a toast to their memory. Now, he was at Hakone Cemetery, visiting EVA's grave. He had dressed for the occasion: his officer's uniform, the same one he wore at the end of Operation Snake Eater, when he was given the title of Big Boss, and a pair of boots. His beret, which revealed his rank, was left in the car.

A bouquet of flowers was in one hand - orchids, EVA's favorite. The legendary soldier walked past the rows of headstones, until he reached EVA's headstone. Crouching down on one knee, he placed them on EVA's headstone. Big Boss placed one hand along the granite and sighed.

The headstone read **TATYANA HAYTER – May 15, 1936 – August 27, 2013**

They had never married, but in most cases, EVA had taken on Big Boss' surname.

'Soon, my love,' Big Boss thought. 'Soon, this war will be over. This will be my final mission. I have been fighting for far too long.'

As his mind searched through the times he and EVA had spent together, one memory stood out in particular.

That night inside the cave, following his escape from Groznyj Grad. He had been tortured by Volgin, and his right eye had been damaged by the muzzle flash from Ocelot's revolvers. After a dramatic escape and a near-death experience in which he encountered The Boss' deceased lover, The Sorrow, he had met up with EVA once again. After tending to his wounds, she presented him with a item that became something of a trademark: his eyepatch.

[Flashback]

Dressed in a bra (or bikini), EVA watched as Big Boss - er...Naked Snake, pick up a spit containing broiled fish. After eating half of it, he switched over to a spit which had some cooked snake.

"Want some?" Snake asked, offering EVA the cooked snake.

EVA kept her arms folded. "No thanks."

"What's the matter? Don't like snakes?"

"Not for dinner," the blonde spy replied as she sat down by the fire.

"Funny. I thought you had to eat them at the KGB."

"We always got the good stuff during training. French, Italian...that kind of thing..."

"You're a regular Mata Hari," Snake noted as he resumed eating.

"You could at least call me Cynthia."

"Tell me something. How does it feel to spy on your own country?"

EVA looked at the flames. "I can't say that it's good. But it's my job."

Snake grunted. "This coming from someone who can't eat a snake during a mission."

The one-eyed FOX operative nearly choked on his meal at EVA's response. "I wouldn't mind eating you."

Snake watched as EVA crawled over to him. Scooting close to him, she smiled at him. "You know, when this mission is over, you'll have to treat me to a nice dinner."

"If we survive," Snake said. "So what you have in mind?"

"How about sushi?"

"Sushi?"

"It's Japanese," EVA explained. "Heard it's all the rage. Supposedly, it's made from raw fish."

Snake grinned. "Raw fish, huh? Been a while since I've visited Japan. Just the place for my survival techniques."

That got a small laugh from EVA. When she turned to look at Snake again, she saw that he was looking at something. Following his gaze, she saw that Snake was looking at a butterfly. He made an attempt to capture it, but missed. With the loss of his eye, his perception was forever altered.

EVA consoled him by embracing him. "Snake...thank you. I'll be your eyes from now on..."

[End Flashback]

"General Hayter?"

The unknown voice had brought Big Boss out of his private thoughts. Big Boss rose to his feet and turned around. Behind him were six men in black suits and shades.

Nerv Department of Security Intelligence, otherwise known as Section 2.

Naomi had left him a message, saying that Gendou Ikari had the men in black combing the city for him. That was two days ago, after Gendou had read the modified dossier.

The lead agent spoke again. "Are you General John Hayter?"

"I am," Big Boss replied. "Who are you?"

"We're with the Nerv Department of Security Intelligence, sir," the lead agent explained, showing him his ID. "Your presence is requested by the supreme commander of Nerv. Come with us, sir."

Big Boss' first chain of thought was to beat the shit out of the Section 2 goons and send their broken bodies back to the Geofront as a warning to Commander Ikari. But his curiosity had gotten the better of him. Besides, he was above Gendou in rank anyway.

'Wouldn't hurt to see what I'm dealing with,' Big Boss thought. 'And I would like to get a look at the Bastard King himself.'

"Fine. Lead the way." the old man said, allowing the men to escort him to the Geofront.

* * *

The Geofront, Commander Ikari's Office.

Seated inside his office, Gendou Ikari was brought out of his private thoughts when his phone began to ring. Retrieving the cellphone from his jacket pocket, he pressed a button and answered it. "Commander Ikari."

"Sir, we have located General Hayter," the lead Section 2 agent reported. "He was at Hakone Cemetery. We are en route to the Geofront."

"Excellent. Was he armed?"

"No, sir. He was not armed."

"Good work," Gendou said. "I will be expecting him shortly."

* * *

Ten minutes later, the six Section 2 agents escorted their one-eyed guest down the corridors of Central Dogma – one in the front, one in the back, and two to each side, to block off his escape.

Big Boss knew the layout of the Geofront, as well as the complex itself. Kaji had proven his worth as a loyal member to the Patriots. But even he knew that Ikari was starting to get suspicious of Kaji's motives, and that he would move against him soon.

Big Boss pushed that thought to the side as he and his escort approached Commander Ikari's office.

After a few moments, the old soldier found himself face-to-face with the supreme commander of Nerv, Gendou Rokubungi Ikari. Behind and to either side of him, was Deputy Commander Fuyutsuki and Ritsuko Akagi.

Big Boss snorted inwardly. 'A scientist running a paramilitary organization. I'm not impressed.'

At his desk, Gendou dismissed the security detail, leaving himself, Ritsuko and Fuyutsuki alone with Big Boss. The elder Ikari sized up the man who was such a positive influence on his estranged son. He knew that Big Boss was a credible threat, and that he had some serious connections within the American and Japanese governments, which meant that trying to eliminate him would be something of a problem.

Gendou tried to intimidate the man with his cold stare. Big Boss wasn't impressed. He looked down at the younger man with his remaining eye, his own thousand-yard stare sending chills down Gendou's spine.

Fuyutsuki looked uncomfortable (and for good reason, since he did try and warn Gendou), while Ritsuko was curious.

After a moment, Big Boss spoke. "So you're the commander, I take it? First meetings warrant an introduction."

Gendou's response was instant. "Who am I is none of your concern."

"Humph. Not that I already know who you are. The other generals talk about you as if you were the devil himself." He cocked his head to the side. "I've seen better, Ikari. Then again, I've seen worse as well."

"That's Commander Ikari to you," Gendou snapped.

"As if you truly deserve that title," Big Boss replied. "One must give respect before it is returned in kind. A second-rate scientist like yourself in charge of a organization tasked with defending humanity from the Angels?" Off Ritsuko's shocked expression, Big Boss continued. "What can I say? My clearance is much higher than your commander, or anyone else's within Nerv. One of the perks of being a General within the United Nations."

Gendou decided to drop that issue. He knew that Big Boss was right. Only a select few knew about Nerv's existence. And that Big Boss was higher than him in rank.

He looked down at Big Boss' dossier, which he had been studying since Ritsuko had found it. "Your military history is quite impressive, General Hayter...U.S. Army...C.I.A...San Hieroyomo...Costa Rica...countless recommendations...even worked as a mercenary. You got around in your youth...for a grunt."

"..." Big Boss remained silent.

Gendou closed his file and assumed his sinister pose. "What is your business with the Third Child?" he demanded.

"Third Child? Oh, you mean young Ikari," Big Boss replied. "Well, he sees me as something of a mentor, since it's pretty obvious that you really don't care whether or not if he lives or dies." His gaze turned on Ritsuko. "None of you."

Ritsuko flinched under Big Boss' stare. "We...we are in the middle of a war," she defended her commander.

"A war which you use children to pilot," Big Boss pointed out.

"They are not children anymore," Ritsuko replied. "If they don't pilot, then we all die."

"And you are?" Big Boss asked, knowing full well who she was, given both Kaji and Shinji's description of her.

"Dr. Ritsuko Akagi, chairwoman of Project E," Ritsuko introduced herself.

"Then you should know that child soldiers deployed into battle on a regular basis is very unhealthy. Nine out of ten children suffering from post-traumatic stress disorder are more likely to snap."

"How do you know? You're not a psychologist," Gendou snapped.

"I worked with children – former child soldiers, before and after the Impact, reintegrating them back into society," Big Boss explained. "Using child soldiers in any war is still illegal, as it was mentioned in the Valentine Treaty, given the use of child soldiers in the wars following Second Impact."

"We are above the law," Gendou said. "We have the backing of the United Nations."

'As well as Seele,' Big Boss thought darkly. "Sure. Construct a weapon that can stand up to the Angels, and the politicians turn a blind eye to the suffering of the pilots, one of which is your son. You unimaginable bastard. You're willing to kill your own flesh and blood."

"What you feel about how I view the pilots means nothing to me," Gendou rebuked. "Nerv's primary mission is to defeat the Angels and to prevent Third Impact."

"Given your precious agency's performance against the last Angel, that is being brought into question," Big Boss dryly noted. "It's the talk among the defense community. Some upstart not only destroyed the Angel, but also made a fool out of two of your pilots."

Gendou was raging internally. Ever since Arael, Nerv had become a laughingstock. Not only did that unknown mecha had destroyed the Angel with little effort, it had also put down both Units Zero and Two, the latter being the most damaged. Since the battle, he had been obsessed with obtaining the mecha in order to exploit its anti-AT technology.

"Oh, the guys at the JSSDF had a field day when they saw the footage of your Evangelions get their asses handed to them on a silver platter. And damn near all of them think that you're a man of ill-repute," Big Boss continued, twisting the knife, watching with amusement as Gendou trembled with silent fury.

Finally Gendou had enough. Slamming one fist down on the desk, he rose to his feet. "Enough! I cannot have you influencing the Third Child. It will affect his ability to pilot. You will stay away from the Third Child."

Big Boss took a step forward. "It seems that you have forgotten your place. You are in no position to tell a senior officer of the United Nations what he can and cannot do."

"General Hayter, you **will** keep away from the Third Child," Gendou threatened, depressing a button on his desk, causing the six Section 2 agents that had escorted him inside to come running into the room. "Or you will not leave this base alive."

Big Boss looked at Gendou. Then he looked at the guards. "Ikari, you have made the biggest mistake of your life."

Then he sprang into action.

Seeing Big Boss perform CQC on video was one thing, but seeing it up close and personal was an entirely different matter. There was no wasted movement. It was like a deadly ballet. Big Boss' moves were quick, brutal precise and professional. Ritsuko and Fuyutsuki quickly got out of harm's way as Big Boss fought the guards. And to top it off, he was pretty strong for an old man, as the six agents found out the hard way.

In less than two minutes, it was over. All six guards were on the ground, some unconscious, others with various appendages broken. Big Boss stood tall, barely winded. Then he saw movement from the corner of his eye.

Within seconds, the old soldier kicked up one of the suits' guns – an H&K P8 – caught it in one hand, aimed and fired.

**BLAM!**

**PING!**

Gendou yelped in surprise – as well as in pain – as his own gun was blasted out of his hand, his hand injured by the shrapnel, the weapon clattering to the floor. Holding his injured hand, he watched with growing fear as Big Boss aimed the gun at his head.

"That was too easy," Big Boss said, having Gendou dead to rights.

Both Ritsuko and Fuyutsuki remained frozen in place. Even more worse, Gendou's office was soundproofed, meaning that no one could hear what was going on inside.

"Commander Ikari, you disappoint me," Big Boss said. "I thought you knew better. Guess I was wrong." He pulled the hammer back. "Section 10, Paragraph 2 of the revised U.N. Charter. Does it ring a bell? Of course not. You probably never read the charter. In any case, here is the shortened version. 'Any officer of the United Nations holding the rank of General is hereby protected under diplomatic immunity.' In other words..."

**BLAM! BLAM!**

Big Boss fired twice, striking the desk, causing Gendou to jump at the impact.

"I can kill you in front of the old man and the fake blonde, and simply walk away," Big Boss explained. "I can walk away and not be charged with shooting you. Your Section 2 would not be able to stop me. You, on the other hand, would be in a whole world of trouble. It's also known within the higher-ups at the JSSDF that you wanted to have a word with me, not to mention that several JSSDF veterans were present at the cemetery when your agents approached. The JSSDF have specific orders to carry out 'Susanoo's Wrath,' should anything happen to me."

"'Susanoo's Wrath?'" Ritsuko repeated.

"Basically, a full-scale invasion of the Geofront," Big Boss explained, keeping his gun trained on Gendou. "With orders to take both Commander Ikari and Deputy Commander Fuyutsuki into custody." His gaze turned from Ritsuko to Gendou, who showed for the first time in his life, pure fear at the one-eyed soldier. "This is your only warning, Ikari," he said, his voice taking on such hardness that even the Devil would be sent running. "You have no idea who you are fucking with. Cross me again...you...will...die."

Big Boss looked down at Gendou, and noticed the dark stains on his crotch. Sneering at the sight of the indomitable Commander Ikari pissing his pants, he dismantled the gun he was holding and dropped the pieces to the ground. A trick that he learned and picked up from after seeing The Boss performs the trick.

"This meeting is over," Big Boss said, turning on his heel and walking out of the office, stepping on several of the injured Section 2 agents that were in his path.

* * *

Central Dogma.

Misato Katsuragi was surprised to see Big Boss leave Commander Ikari's office. "General Hayter, what are you doing here?"

"Your commander invited me for a 'friendly chat,'" Big Boss replied, his mood a complete 180. "It really didn't end too well for him."

Misato's eyes widened. "You...you didn't..."

"Calm, Major. He is still alive," Big Boss said. "Although...he would think twice in trying to threaten a General of the United Nations with death. Especially me." He took several steps forward, then stopped and turned around. "Walk with me, Major."

"Sir." Misato followed the old man.

* * *

The old general and the young major traveled along the moving walkways that were used inside Central Dogma. "It is apparent that Ikari dislikes the positive influence I have regarding to Shinji," he noted as he lit up his cigar and took a puff. "That pathetic excuse for a commander wants someone who can easily be controlled. I meant it when I told you to be wary about Commander Ikari."

"I have been for quite some time," the ponytailed major replied. "Ever since the Dummy Plus fiasco in Matsushiro. I can see why Shinji hates him."

"Smart move. Not everything is as it seems, Major," Big Boss said, taking a drag from his cigar. "Are you aware that Ikari was present at Mount Markham?"

Now that, Misato did not know. "No...that's news to me."

"He was known as Gendou Rokubungi at the time," Big Boss explained. "Following Second Impact, he had married Shinji's mother, and taken on her family name."

"Shinji told you that?" Misato asked.

"No. I read his file. One of the perks of being a general is that you get to know who's who in the defense business," Big Boss explained. "The movers, and shakers, if you will."

"So what happened between you and Commander Ikari?"

Big Boss gave her a brief explanation detailing the chain of events which led to six broken bodies and a slightly injured supreme commander, as well as the ramifications of Gendou's threat towards the old man. By the time Big Boss had finished his explanation, they had reached the entrance. Outside, Big Boss' car was waiting for them, the driver an enlisted peon with the JSSDF.

"If I were you, Major, I'd find out who are truly your friends," Big Boss said. He then said something that was to Misato, prophetic. "The day of reckoning is coming, and soon."

Misato was left to ponder Big Boss' words as he entered the car. Nodding to the driver, the driver pulled off.

* * *

Nerv Headquarters, the Geofront, the following day.

It was another Angel attack. As it was back with Zeruel, it was inside the Geofront. This time, Gendou had ordered Unit One to be taken out of cryo-stasis and Shinji placed back on the active roster. Within minutes, all three pilots were in their EVAs and were dispatched to the Geofront.

Inside the bridge, the bridge bunnies, Misato, Ritsuko, Gendou and Fuyutsuki were watching the three EVAs on the monitor. Naomi was for some reason, absent.

"Where's the Angel?" Asuka demanded.

"Maya, talk to me," Ritsuko commanded the female bridge bunny.

"The wavelength has vanished, Sempai," Maya said. "I got nothing."

It was at that moment, the deception was revealed.

The computers went nuts as the blue pattern returned. Maya was on it in an instant. "The wavelength is back!" Her eyes widened in horror as to where the origins of the wavelength were coming from. As she backed slowly from her console, she said, "It's...it's...Pilot Ikari!"

The entire bridge went silent at Maya's proclamation. You should literally hear a pin drop. Gendou slowly rose from his seat, concern etched across his face for the first time. Fuyutsuki and Misato both had worried expressions on their faces, while Ritsuko looked pale. Even Units Zero and Two were looking at Unit One, both female pilots aiming their palette rifles at the supposed Angel.

"Hahahahahahaha..."

Almost immediately, Ritsuko punched in several keys on Maya's console. Within seconds, a video feed from inside Shinji's Entry Plug was on the screen.

Sure enough, Shinji was chuckling, as if he had caught the joke. Little did they know was that the joke was on them.

"Ikari...?" Rei whispered, looking at the video of Shinji's plug.

"Oh, wunderbar. The baka's snapped," Asuka sniped, also doing the same.

Then Shinji spoke. "Sharp knife. Sharp knife to send him to Deep Temple. Flay...and say...my words. Abdul comes again, on the Feast of the Weaker. Feast for the Deep Temple."

When he looked up, the gathered audience gasped in shock.

Shinji's eyes had changed. Red irises, similar to Ayanami's but with one major exception.

The whites of his eyes were now black.

"Born again, here. Alhazzared. G'yeth. G'yeth," Shinji finished.

"Dead God..." Fuyutsuki whispered.

Shinji answered their unspoken question. "They came to me," he rasped, his voice becoming distorted. "The Angels. They made me a deal. I destroy this place, and all of you, in exchange for not only their power, but Third Impact will be avoided and humanity will be spared. I accepted their offer."

"Shinji!" Misato pleaded. "Shinji, no! Don't do this!"

"Shinji is not here right now," the pilot replied. "There is only Azrael, the Angel of Vengeance!"

Gendou was quick to act. "Terminate the pilot's connections. Increase LCL pressure to maximum," he ordered Makoto.

The bespectacled male bunny rushed to obey. However, something went wrong. The screams of Asuka and Rei echoed throughout the bridge, which was followed by both Units Zero and Two jerking violently before going limp, their rifles falling to the ground. Shinji then showed them the video feed from inside their Entry Plugs. Both Asuka and Rei were out cold.

Shinji/Azrael chuckled softly. It was easy to simply switch the signals from his Unit One to Units Zero and Two and watched as both Sohryuu and Ayanami fall victim to the increased LCL pressure.

"You fooled me once with that little stunt, Rokubungi," Shinji/Azrael said. "I will not fall for that trick again."

Shinji snapped his fingers. As the bridge watched on, both retractable plates on Units Zero and Two blew open, their Entry Plugs ejecting. Unit One caught both of them in its hands.

Gendou was on Maya in an instant. "Damn it; terminate the Third Child's connections! Now!"

Maya was already performing the task, but to no avail. "I'm trying, Commander! He's locked me out of the system!"

Shinji/Azrael chuckled as he watched Maya try to wrench control from him. "Just what do you think you are doing, Maya?" he deadpanned, as his eyes glowed a demonic red. "I can't let you do that."

Ritsuko looked at Shinji, and then at Maya, who was typing away. Almost immediately, she knew what Shinji had planned. "Maya! Get back!" Ritsuko shouted.

It was already too late.

The protégée of Ritsuko Akagi was glued to her seat, her body violently jerking as electricity surged through her body, her screams echoing throughout the bridge. Misato held Ritsuko back while Makoto and Shigeru scrambled back from their own consoles.

**BOOM!**

Maya's body went flying back as her console exploded, landing on the floor, eyes vacant, her face in a mask of eternal pain and riddled with shards of broken glass, her bowels letting loose on the floor, her body twitching several times before it went still.

She was dead.

"Do I have your attention now, Rokubungi?" Shinji/Azrael inquired. "Good. Now pay attention to this..."

The remaining bridge members watched as Unit One held both Entry Plugs containing the still-unconscious pilots within with one hand. In the other, was a palette rifle.

Misato saw the evil look on her former ward's face and knew what she had planned. "Shinji, NO!" she screamed.

"SHINJI, WAIT!"

This time, it was from Gendou. "Please, don't do this!" he pleaded. "I'm sorry for abandoning you! I'm sorry for forcing you to pilot EVA! I'm sorry for what I did to your friend! I'm sorry for everything! Just let Rei go!"

Even though seeing Gendou beg was a once-in-a-lifetime event, Shinji/Azrael had no pity.

He tossed the plugs into the air.

"NO!" Misato, Ritsuko, Gendou and Fuyutsuki shouted at the same time.

Two three-round bursts from the palette rifle had done its damage. And the people inside the Nerv Geofront had a front-row seat as to the deaths of Rei Ayanami and Asuka Sohryuu.

Asuka's head had exploded into a red mist, while nearly everything from the waist up was gone from Rei. The two Entry Plugs landed on the ground, leaking LCL and blood.

Shinji/Azrael then turned to the black pyramid that housed Nerv Headquarters. A weapons rack rose from beside him and the Angel dropped the palette rifle and retrieved a far deadlier weapon.

A massive Gatling gun, similar to the one he used on Shamasel, complete with a 100-round drum.

Shinji/Azrael's smile grew even more sadistic as he aimed for the pyramid. "Aim at the center target, switch," he whispered.

Without warning, Shinji/Azrael opened fire, riddling the structure with massive HE Rounds, killing the majority of the personnel inside. Misato had ducked, and had avoided the salvo of death that the Angel of Vengeance rained down upon Nerv. By the time the ammo was spent, the pyramid that housed Nerv Headquarters was reduced to Swiss cheese, the bridge once again exposed to the outside world.

Somehow, whether it was through luck or divine intervention, Misato Katsuragi had survived. The others were not as lucky. Body parts that were Gendou Ikari, Kouzou Fuyutsuki, Shigeru Aoba, Makoto Hyuuga and Ritsuko Akagi littered the destroyed bridge, and countless more lay dead within the corridors of Central Dogma.

Staggering to her feet, Misato looked at the carnage left in Unit One's wake.

"_Daisy...daisy..._"

**CRASH!**

Misato spun around, just in time to see Unit One's outstretched hand engulf her, lifting her out from the destroyed bridge. The sole survivor soon found herself face-to-face with the horned face of Unit One.

Shinji/Azrael was singing, as Unit One held her in its grip. She tried to break free, but with little success. "_Give me your answer do. I'm half-crazy, all for the love of you. It won't be a stylish marriage, I can't afford a carriage. But you'd look sweet upon the seat...of a bicycle built for two._"

"Shinji, please...let me go," Misato pleaded.

"I can't, Major Katsuragi," Shinji/Azrael said in a soothing tone. "But fear not. For you will soon be reunited with your father. Don't be afraid."

Misato's eyes widened as to what the insane pilot of Unit One had planned.

Her fears were verified when the only working warning klaxon erupted and the only working speaker said the following. "Warning. Core overload detected in Unit Zero, Unit One, and Unit Two. Self-destruct imminent. Self-destruct in five...four...three...two...one..."

"SHINJI, NO!" Misato screamed.

For a moment, Misato saw the three EVAs morph into three glowing, giant white versions of their respective pilots, naked, right before they exploded simultaneously. Their destructive power increased threefold, the massive explosion not only wiped out the Geofront, killing those that had managed to survive Shinji's barrage of firepower, but rose upwards, all of Tokyo-3 disappearing in the deadly blast.

* * *

Misato screamed as she sat upright in her bed, kicking the covers away from her body. It took her a moment to recognize that she was not in the Geofront, but rather her own bedroom. Asuka was out at Hikari's for the weekend, allowing her some time for herself.

Misato took in several deep breaths, trying to get her heartbeat back to normal. She remembered her run-in with General Hayter earlier that day, which was followed by her checking on Gendou - as well as the six men - who was getting his injured hand treated by Ritsuko, while the six men were worked on by Naomi.

After a dry-heave episode inside the bathroom, Misato staggered back into her bedroom.

'Oh, God,' she thought. 'What a horrible nightmare.'

It would be another hour before Misato could finally get some sleep.

* * *

At the same time, JSSDF Base Haruna, outside of Tokyo-3...

FOXHOUND has just arrived in Japan.

Big Boss and Ocelot watched as the Nomad slowed to a stop inside the hangar. Following the interrogation of Fuyutsuki, Ocelot had summoned FOXHOUND to Tokyo-3 in order to prepare for the final battle against Seele. The Nomad's back ramps opened and the special forces unit disembarked from the plane.

Solid Snake and Meryl exited together, followed by Raiden, Otacon, Jonathan, Ed, Mei Ling and the four Beauties.

Father and son exchanged salutes, followed by a handshake. "Snake."

"Big Boss." To Ocelot, Snake said, "Ocelot."

"Snake," Ocelot replied.

"Welcome to Japan," Big Boss said. "How was the flight?"

"Boring," Snake replied. "Nothing but ocean."

"Tell me about it," Big Boss said. "I always hated flying. FOXHOUND's been keeping track of the Angel attacks in Tokyo-3?"

Mei Ling nodded. "Yes, General. Pretty freaky stuff too."

"Just call me Big Boss," the old man insisted. He then addressed the gathered members of FOXHOUND. "We are in the final stages of this war for humanity. And despite having the complete backing of the JSSDF, the RAYs, and all of you, Seele may have some surprises in store, which is why I am not taking any chances."

Turning on his heel, he beckoned the others to follow him.

* * *

Briefing Room.

The ten members of FOXHOUND settled in their seats as Big Boss conducted the briefing, complete with a slide projector. Naomi Hunter was also present, as she told Ritsuko that she would be meeting with an old flame who worked on the Haruna base. The three JSSDF generals who were at Mount Futagoyama were also present, as was Ryouji Kaji.

"As you already know, the RAYs have been launching tactical precision strikes against Seele's interests," Big Boss said. "And several weeks ago, the Seele mountain facility which has housed both the mass-production Evangelions and Tabris has been completely destroyed. But we're not out of the woods yet. We simply destroyed Seele's main option for unleashing Third Impact. Now, more than likely, Seele will probably launch an invasion of Nerv in order to wrestle control of Third Impact from Gendou Ikari."

Big Boss pressed a button, and Gendou's picture and dossier came up on the screen.

"Gendou Rokubungi Ikari. Supreme Commander of Nerv, and member of Seele. Born 29 April 1967 as Gendou Rokubungi. Took on his wife's surname shortly after marrying Gerhim bioengineer Yui Ikari. Former protégé of Kouzou Fuyutsuki, the current Deputy Commander of Nerv. Has one child, a son - Shinji Ikari, and is the guardian of Rei Ayanami, both of which are pilots of the EVAs. He is also responsible for sabotaging the Contact Experiment that was conducted by the Katsuragi Research Expedition on Seele's orders, thus triggering Second Impact. Through the interrogation of Deputy Commander Fuyutsuki, Gendou is planning a controlled Third Impact in an attempt to reunite with his wife, at the cost of every living being on the planet."

Laughing Octopus scoffed. "Second Impact was bad enough, Boss. I still have nightmares of that hell."

"I concur with Octopus," Crying Wolf added. "So what is the plan?"

"There is one more Angel remaining, designated Armisael," Big Boss explained. "Once the last Angel is destroyed, both Seele and Ikari will turn on each other. Seele already has the Haven Shock Troops on standby, seeing as how they can't completely trust the JSSDF, and for good reason, since the JSSDF is loyal to The Patriots."

"So what is the plan?" Screaming Mantis asked.

"Obviously, Ikari must be stopped, since he has ADAM in his possession," Big Boss replied.

"ADAM? The progenitor of the Angels? I thought he was destroyed in Second Impact," Raging Raven said.

Big Boss shook his head. "The purpose of Second Impact was to revert ADAM into an embryonic state, thus making him far more easier to control. Once Gendou finds out that Tabris is not coming, then he will use the forbidden union of ADAM and Lilith to unleash Third Impact."

"Which will create an anti-AT-field strong enough to negate the AT-field of every human being, reducing humanity to LCL and allowing Lilith to absorb the souls into her Black Egg," Otacon finished.

Big Boss nodded. "Exactly, Doctor Emmerich. In the meantime, get settled in. I have a call to make. Dismissed."

* * *

A meeting of the Human Instrumentality committee was taking place. Rather than the typical twelve monoliths, the committee consisted of the five senior members of Seele, communicating via holograms. Keel sat at the head of the table, while the American and British representatives sat at Keel's left, while the French and Russian representatives sat at the right. The far end of the table was for Gendou Ikari.

Only this time, Gendou wasn't here, as was the French representative, who was one of the Seele members killed before the invasion of the Tarumae facility.

At the moment, footage of the battle against Arael, and the following battle against Unit Two was being played.

"We have identified the mecha," the Russian representative said. "It is a variant of a pre-Second Impact weapon known as Metal Gear."

At that, Keel looked up. "Did you say Metal Gear?"

"Yes, Chairman," the Russian replied. "The original schematics were designed by..."

"Granin," Keel said. "Aleksandr Leonovitch Granin. Former director of the 0KB-812 Granin Design Bureau. Was twice awarded the Order of Lenin and the Stalin Medal. Killed fifty years ago in the former Soviet Union by renegade Soviet Colonel Yevgeny Borisovitch Volgin."

"Yes, Chairman," the Russian replied. "How do you know this?"

"Simple. The American and Russian governments have recently declassified several documents pertaining a secret operation called Operation Snake Eater," Keel explained. "Naturally, the documents came across my desk. Please continue."

"This variant of Metal Gear is known as Metal Gear RAY," the American continued. "It was originally designed by the U.S. Marine Corps as a countermeasure for the abundance of Metal Gears that were being developed following the Shadow Moses Incident of 2005. Following the Manhattan Incident of 2009, the number of Metal Gear copies dwindled down to almost nothing. What we have seen here with the attack on the Tarumae Facility and in Tokyo-3 is the next-generation models of the RAYs."

"From the look of things, they have been outfitted with anti-AT technology, given how easily it can penetrate the EVA's AT-field," the British representative said, "not to mention that it destroyed Arael in one shot."

"Is this Ikari's doing?" the American asked.

It was at that moment, the seat on the opposite end of the table lit up, signaling the arrival of Gendou Ikari.

Only problem was, it was not Gendou seated at the opposite end.

It was Big Boss.

"No. Not Ikari," Big Boss deadpanned. "It's mine."

Keel and the three remaining representatives turned to the newcomer.

"Who are you?" the British rep demanded.

"This is a secure line," the Russian added. "How did you...?"

"Easy. I simply jacked the line," Big Boss replied. "It's not that hard really."

"So...you're the one responsible for the destruction of the Tarumae facility," Keel said. "As well as the orchestrated strikes against our interests all over the world."

"That's right," the legendary soldier admitted.

"Have you any idea what you have done?" the Russian shouted. "Those mass-produced Evangelions were our key for achieving Instrumentality!"

* * *

JSSDF Base Haruna, outside of Tokyo-3.

Inside a hidden computer room, Big Boss sat at a desk, while the techs worked around him. Ocelot was also present, and listening in with a pair of headphones. The techs' tasks were simple. Hack into Seele's signal and project an image of Big Boss that would show up at the next committee meeting.

Snake and Meryl showed up minutes later, having been escorted there by a JSSDF tech. The two FOXHOUND operatives kept silent as Big Boss continued to speak with Keel.

"No, your goal was to avoid a natural death by ascending into godhood," Big Boss rebuked. "At the cost of every living being on this planet. Second Impact wasn't enough for you, wasn't it?"

"It was a means to an end," Keel replied.

* * *

Back inside the meeting room, Keel continued. "You act so high and mighty, yet your hands are stained with the blood of the people you yourself had killed."

"Only difference is that I did not kill two billion people in an instant, Chairman."

"True," Keel admitted. To the other members, he said, "Leave us. I wish to speak with this man alone."

One by one, the three representatives blinked out of existence, leaving only Keel and Big Boss. Clasping his hands together, the Seele chieftain looked at his Patriots counterpart. "I never thought that you survived Zanzibarland...Jack. Or should I call you...Naked Snake?"

Big Boss' eyebrow raised Spock-style. "You know me?"

"I should," Keel replied, dropping the German accent in favor of a crisp British accent. He removed the visor, allowing Big Boss to get a good look at his face.

Big Boss's eye went wide at the revelation that sat across from him. The face was older, much older than Big Boss and Ocelot were, the eyes white and lifeless, but he recognized that scar over the left eye from anywhere.

"This fox is still one step ahead of the hounds." Keel said.

Big Boss recognized that line. It was during his stay in the hospital following the disastrous Virtuous Mission that he received a visit from his commanding officer, Zero.

[Flashback]

Some 50 years earlier...

"So, how does it feel to be a patient in one of the most advanced ICUs in the world?" Major Zero asked as he entered the room, looking at a banged-up and bruised Naked Snake.

"Would you do me a favor and tell the suits about visiting hours?" Snake sniped as he sat up in his hospital bed. "I'll never get better with them assaulting me day and night with their questions."

"Must be part of the top brass' inquiry about the failed mission," Zero mused.

Snake snorted. "More like an interrogation. According to them, I'm a traitor and an accomplice to The Boss' defection."

"Calm down, Jack. They're simply looking for a scapegoat."

"So what does that mean? The top brass is after you too?" Snake asked.

Zero smiled. "Let's just say neither one of us is going to be made a national hero out of this."

"So what happens now? Is FOX going to be disbanded?"

"I wouldn't worry about that," Zero replied. "Besides, this fox is still one step ahead of the hounds."

[End Flashback]

It didn't take Big Boss too long as to who he was talking to. "Zero..."

Keel, or rather, Zero, placed the visor back over his eyes. "It's been a long time, Jack. Too long. Here, I thought I had your remains on ice. Instead, you pulled the wool over my eyes."

"As did you," Big Boss replied. "You should have died when Old Tokyo was destroyed."

"I almost did," Zero admitted. "I was in Old Tokyo being retrofitted with implants that would keep me alive. When the bomb struck, I saw this as an interesting opportunity to...reinvent myself. Thus, Zero died, and in his place, is Keel Lorenz, chairman of Seele."

"..." Big Boss was silent.

"Cat got your tongue, Jack?" Zero taunted. "Maybe I should start from the beginning..."

[A series of flashbacks, done in the MGS-style of artwork. The first is of the Dead Sea Scrolls being discovered in Israel. Zero is among the research team, only he is a soldier himself.]

ZERO: (voice-over) It was during the last years of the British occupation in Palestine that the Dead Sea Scrolls was discovered inside a cave near the ruins of Khirbhet Qumram. I was but a lieutenant in the military at the time.

[Picture of the younger Zero discovering the Secret Dead Sea Scrolls, otherwise known as the War Scroll.]

ZERO: (voice-over) Within the scrolls, I stumbled upon a hidden scroll. That scroll foretold the coming of the Angels, Second and Third Impact, as well as the Evangelions. It was after I had made it safely back to England, that I came across several people who had caught wind of the scrolls in my possession, those that believed that humanity has reached its peak and is stagnating.

[Picture of the twelve members of Seele, Zero himself at the head. Instead of the monoliths, we see the council of twelve seated at a round table.]

ZERO: (voice-over) Thus, Seele was formed, the founding members were former members of the Philosophers. I assumed the role of Keel Lorenz, a German industrialist who turned against the Nazis in the Second World War, given the fact that I played the role of a German during the war. Of course, we simply had to bide our time, and wait.

[Shot of Zero and The Boss' lover, The Sorrow.]

ZERO: (voice-over) However, my plans were discovered by your mentor's lover.

BIG BOSS: (voice-over) The Sorrow? Ocelot's father?

ZERO: (voice-over) One and the same. He found out about the War Scrolls and had planned on stopping me. I knew that he was close to The Boss, given how she had gave birth to that bastard child of theirs on Omaha Beach. If he told The Boss about my plans, then I had to eliminate them both.

[The photo of The Boss and The Sorrow in Tselinoyarsk.]

ZERO: (voice-over) It was easy to manipulate The Boss into eliminating The Sorrow. She followed her orders like the perfect little soldier that she was. She never asked questions, nor did she wondered where the order came from to eliminate The Sorrow. Eliminating The Sorrow had broken her. Then came the mission to steal the Philosopher's Legacy from Volgin...

[Shots of Volgin firing the Davy Crockett at Sokolov's facility.]

ZERO: (voice-over) I had my concerns in regards to The Sorrow warning The Boss of my intentions, but you know me, Jack. I am never one to take any chances. So I contacted Volgin through the back channels and notified him of not only The Boss' defection, but that she would be carrying two mini-nukes. He got he idea of firing the nuke on his own. And it gave me the perfect excuse to eliminate the last remaining threat to my plans.

[Cut to the present. Big Boss is not very happy. In fact, he is Pissed with a capital P. Les Enfant Terribles was bad enough. Now, it appears that Zero has been toying with Big Boss for most of his career.]

ZERO: (voice-over) I do feel some regret over my decision to have you kill The Boss. But it was for the greater good. Did you really think that order came from the top brass? No, Jack, no. Those orders were mine. The Soviets had no intention of launching their nukes should you failed in killing The Boss. They knew that Volgin was responsible. What I told you was simply a bluff. Even the men who questioned you while you were in the hospital were on my payroll. I simply needed you to do some wet work. President Johnson didn't know what was going on. He thought that the Russians were a threat, when in truth, they were not.

[Cut to the photo of The Patriots. The same photo that Shinji was looking at back in Big Boss' home.]

BIG BOSS: (voice-over) And the original Patriots? What about them?

ZERO: (voice-over) I had high hopes for all of them. Clark...Signt...Ocelot...even EVA and yourself. But Para-Medic and Signt...they got too greedy. EVA and Ocelot...they wallowed in their self-righteousness. And then, there's you, Jack. You were supposed to be the face of the Patriots. But you just couldn't play along.

BIG BOSS: (voice-over) And what of The Boss' dreams?

[The cutscenes end here. We go to Zero, still in his chair.]

"Don't misunderstand, Jack," Zero replied. "I respected The Boss a great deal. I still do. I have not deviated from her ideas of a world united, no. Far from it, humanity needs to take the next step forward, and what better way to unite the world is through Human Instrumentality? I'm not destroying the world, Jack. I'm saving it."

"You're mad," Big Boss muttered. "You completely lost it. You killed EVA and Roy back in Prague."

"And I also regret that," Zero said. "But it was necessary. I could not let them or you stop my plans, not while I am so close. You fail to see the big picture here, Jack, and that is your ultimate flaw. You tried to stop me before, and you failed...in Outer Heaven and in Zanzibarland. Walk away, Jack. Walk away and let the future of humanity commence. This is your only warning."

* * *

Inside the JSSDF facility, Big Boss sat at the chair for a long moment. His hands balled into fists as his eye showed nothing but rage. Ocelot was also furious, but it was clear that Big Boss was the more angrier of the two.

"Excuse me," the one-eyed legend hissed through clenched teeth as he stood up. "I need...to get...some air."

He stalked out of the room, the techs clearing a path for him. Snake and Ocelot soon saw why.

Big Boss was holding The Patriot in one hand.

"What happened?" Snake asked, knowing full well that whenever Big Boss was pissed, he would go shoot something. "Ocelot, what happened?"

"Zero..." Ocelot replied. "Keel Lorenz of Seele is Major Zero."

Meryl blinked. "You mean that the Chairman of Seele is the guy who founded the Patriots?"

Ocelot nodded. "It gets worse. I'll fill you in on the details. Right now, we got to find Big Boss before he - "

A yell of pure rage was heard throughout the base, which was followed by gunfire.

"Too late," Meryl gulped.

* * *

Outside, Big Boss was venting his frustrations in the only way he knew how.

By blowing shit up.

So far, he has destroyed two cars with his Patriot, and was working on a supply truck, which was thankfully empty as he riddled the vehicle with bullets. On their way to Big Boss, Ocelot had explained what had transpired in the meeting between Big Boss and Keel, now revealed to be Zero, which led to Big Boss destroying JSSDF property in a fit of rage. And the old man had gained an audience in the form of the other FOXHOUND members and the generals, who had told everyone else to keep away.

Holding the Patriot with one hand, Big Boss had struck the gas tank of the truck, causing it to explode, forcing everyone to take cover from the blast.

His rage spent, Big Boss dropped the Patriot, and sank to his knees. "God...damn...it..." he muttered.

* * *

One hour later...

Following his rampage, Big Boss had stalked towards a dorm building that was used by the JSSDF officers. Since the majority of them were in Tokyo-2 on a training seminar, the dorm was empty. The old man had claimed an empty dorm room for himself and had refused to come out, leaving Ocelot and FOXHOUND inside the common area.

Ocelot had explained to the gathered members the horrifying truth about what Zero had told Big Boss during the meeting.

Needless to say, everyone was shocked.

"Big Boss never got over the fact that he had executed The Boss," Ocelot finished. "He told me...that the battlefield took the pain away. He buried it down deep for fifty long years." His hand clenched into a fist. "Now...thanks to Keel, no make that Zero...the guilt is back in full force." He sighed. "Zero always knew how to press Jack's buttons. He's used Jack to kill The Boss. He used Snake to infiltrate Outer Heaven, when Jack's original intention was to invite Snake in."

"Wait...Big Boss was going to invite me into Outer Heaven?" Snake asked, shocked.

Ocelot nodded. "That was Big Boss' intention. But Zero thwarted that, since he saw Big Boss as a threat to his power."

"So what's your role in this little war?" Meryl asked. "Given your past history with Snake and myself, you are not exactly trustworthy. But the real question is how you met Big Boss and why does he trust you, of all people?"

"True. I was trained to be a double agent, originally by the Philosophers, the predecessors to The Patriots," Ocelot explained. "I was sent into Russia in order to steal the Philosopher's Legacy - the combined war chest of the United States, Russia and China, worth about $12 billion back in those days."

[Another fade out. We're back to clips from both the Virtuous Mission and Operation Snake Eater. Only this time, they are centered around the younger Ocelot.]

OCELOT: (voice-over) I met Big Boss fifty years ago when he was first sent to Tselinoyarsk to rescue Sokolov. Of course, he wasn't known as Big Boss back then. He was known as Naked Snake. I was originally ordered to contact him, but I was unable to, since I was in too deep as a member of Volgin's faction. I was the major of the Ocelot Unit, assigned to guard Sokolov, the designer of the Shagohod.

[We see Naked Snake schooling the young Ocelot in CQC, after the latter's Makarov jams.]

OCELOT: (voice-over) I had my first taste of CQC, albeit I was on the receiving end, though. But he did give me some good advice.

NAKED SNAKE: You ejected the first bullet by hand, didn't you? I see what you were trying to do. But testing a technique you only heard about in the middle of battle wasn't very smart. You were asking to have your gun jam on you. Besides, I don't think you're cut out for an automatic in the first place. You tend to twist your elbow to absorb the recoil. That's more of a revolver technique.

SOLID SNAKE: (voice-over) You mean to tell us that it was Big Boss that got you into revolvers?

OCELOT: (voice-over) It was a trial and error process. But yes, Big Boss inspired me to use revolvers.

[Next scene is that during Operation Snake Eater. Ocelot is holding EVA hostage with one hand, while he is holding a nickel-plated Colt revolver in the other. He tries to fire on Snake, but is empty, allowing EVA to kick the crap out of him, which leads to her running Ocelot down with her bike.]

NAKED SNAKE: That thing only carries six shots. The Makarov carries eight. You have to get a feel for how many you have left. This is a high class weapon. It's not meant for shooting people.

[The battle at Bolshaya Past Crevice.]

OCELOT: (voice-over) By the third time I ran into Big Boss, I was ready, but the fight was called off due to outside interference.

[Said interference in question was The Pain's hornets. Ocelot holds them at bay by spinning his revolvers. Naked Snake is slashing at them with his CQC knife. The Ocelot soldiers are being stung to death.]

OCELOT: (voice-over) Ever wondered how he got that eyepatch?

OTACON: (voice-over) That was your doing?

[The torture room inside Groznyj Grad. Snake body-checks Ocelot as he juggles his revolvers, causing one of them to go off, the muzzle flash blinding Snake in his right eye.]

OCELOT: (voice-over) I do feel bad about that. Snake was captured and was later tortured by Volgin. I suspected that EVA was a spy and I decided to test her. The muzzle flash from my revolver blinded Big Boss in the eye. It was EVA who presented him with the eyepatch after he had escaped. Ironically, it was through Big Boss getting tortured that I became a specialist in 'interrogation techniques.'

[After Volgin leaves, Ocelot jams a transmitter into Snake's shoulder.]

YOUNG OCELOT: So you survived the colonel's torture, eh? (claps his hands) Watching this has made me realize something...it's really not that bad. It's the ultimate form of expression.

[The footage of Snake Eater ends here. Now we see Ocelot approaching Big Boss.]

OCELOT: (voice-over) Zero had invited me to join the Patriots, along with Donald Anderson and Dr. Clark. I, in turn approached Big Boss and asked him to join us in creating a new world. A world in which there was no East and West. No capitalism nor communism. A world envisioned by The Boss herself. A world united.

[Now we see Big Boss training Ocelot in CQC.]

OCELOT: (voice-over) Big Boss took me on as his student. He trained me in close-quarters-combat, as well as how to become a more effective soldier. I admire and respect that man a great deal, and still do to this very day.

[Here, the scenes end and we go back to the present.]

"Not only is he dealing with the guilt of killing The Boss," Ocelot concluded, "but Zero has shaken his faith in seeing this mission through. Like it or not, we need Big Boss." He turned to the closed door. "I think, that most of all, he wants to be forgiven for killing The Boss."

"That's kinda hard," Snake said mildly, "given the fact that The Boss has been dead for half a century."

"Hard, yes, but not for a spirit medium."

Everyone turned to Screaming Mantis. The leader of the Beauty and Beasts Unit rose to her feet. "If it's absolution that Big Boss wants, then he shall receive it. Wait here."

The South American woman departed from the common room.

* * *

Mantis stood before the door. Beyond said door, was a brooding Big Boss. She knocked on the door.

"Go away," came the reply.

Mantis ignored the retort and entered the room. There, seated on the edge of the bed, shoulders slumped, was Big Boss.

"Sir..." Mantis began, "We know everything. Shalashaka explained it to us."

"Did he now?" Big Boss deadpanned.

"Big Boss, please listen to me," Mantis pleaded. "You can't give up now. If you do, then all of this has been in vain."

"You're still young," Big Boss replied. "You have no idea what it feels like to be betrayed."

"But I do know what it's like to lose someone you care about," the woman replied. "You, along with Ocelot and EVA, saved my life following Second Impact, and I never thanked you for that."

"..."

"She's here, you know," Mantis said. "The Boss. She always has been watching over you in the field of battle. She does not hold any ill will towards you."

That caught Big Boss' attention. "What?"

"Consider this my appreciation for helping me," Mantis said as she placed one hand on Big Boss' shoulder. "Soon, you will pass on into the dreamscape. There, The Boss awaits."

Big Boss started to say something, but his eye felt heavy. Mantis' powers were working. Soon, his head slumped forward as he lost consciousness. Mantis gently laid him out on the bed before exiting the room.

"Well?" Ocelot demanded, having followed her out of the common area.

"He will be fine in a couple of hours," Mantis replied. "All we can do is wait."

* * *

Within Big Boss' subconscious...

_"The spirit of the warrior...will always be with you. Don't be sad...we'll meet again someday."_

Big Boss's eye snapped open. He found himself looking at the clear blue sky. Upon sitting up, he saw that he was in a field. A field full of white flowers, right next to a large lake. A dead tree was nearby.

Big Boss recognized the place instantly.

Rokovoj Bereg.

The name translated to 'Fatal Coast,' which was fitting, given that he had fought and killed The Boss here.

There were some things that Big Boss had noticed. One, he had de-aged fifty years. Two, he was dressed in the Tiger Stripe camo, complete with the bandanna around his head. Three, he still had that eyepatch.

"It's been a long time, Jack," a female voice said from behind.

Big Boss turned around. Standing less than six feet from him, was the woman whose ideals helped shape his life.

The Boss.

She was dressed in the same white prototype Sneaking Suit he had seen her in during Operation Snake Eater. Hair pulled back in her ponytail. Her weathered face still as he remembered.

"Or should I call you...Big Boss?" The Boss continued. She gave him a small smile. "It does have a nice ring to it."

"Boss..." her former protégé choked out. "I...I..."

The Boss silenced him. "You don't have to say anything, Jack. I know what it is you want. You wish to be forgiven for taking my life."

Big Boss slowly nodded. "More than anything."

The Boss walked over to Snake and places one hand on his shoulder. "Jack...you've carried the burden of what happened here for far too long. I never blamed you for what happened here. Now, the world is at risk because of Zero and Seele. My son...your son...they both need you to lead them to victory."

"Zero...he used you to kill The Sorrow...used me to kill you..."

"I know, Jack. I know. I've watched you grow into a soldier worthy of carrying on my name, and legacy. It's time for you to move on, Jack. Don't grieve for me. You have a duty to humanity to perform. Stop Zero and Seele from unleashing Third Impact. Avenge my death. Avenge those that Zero has wronged. Now go. You have a duty to perform, Jack."

Big Boss nodded. "Boss...thanks."

The Boss nodded. "Always remember that I will always be watching you. Good luck, Jack."

* * *

JSSDF Officers Dorm, later...

Ocelot and Snake returned to the quarters when Crying Wolf noticed the smell of cigar smoke in the air, signaling that Big Boss was awake. The door was open, allowing Snake and Ocelot access.

Sure enough, Big Boss was awake, and smoking a cigar. Snake and Ocelot saw that the doubt and guilt that Big Boss had was gone. Whatever Screaming Mantis had done had worked, since the proverbial Sword of Damocles was lifted from Big Boss' shoulders. The old man's eye showed determination that neither Solid Snake nor Ocelot had seen in years.

"Boss?" Ocelot began. "You okay?"

Big Boss blew out a puff of cigar smoke. He only said four words to both Snake and Ocelot.

"Zero is going down."


	7. Episode 6: Bitter Tears

_**Episode 6: Bitter Tears**_

Snafu's Notes: Holy crap. I never knew that my Eva/MGS x-over would be this popular. Zero as Keel was something that came to me at the last minute. Had to carry on the tradition of plot twists in Metal Gear...aside from the obligatory piss-your-pants shtick. Not as good as the twists Kojima the Great would pull regarding his beloved series, but I'm getting better at it. You wouldn't believe the PM's I got as a result of throwing that little curve.

The previous chapter also had several references, in case you dear readers did not see. I used Jamie's Diary from Fallout 3 in which Shinji recites when Maya reveals that he is Azrael (I love that game). I also used that line in the Ranma fanfic (or bashfic) Pride Comes Before The Fall. The other reference is Shinji singing 'Daisy Bell,' an obvious reference to 2001: A Space Odyssey, right before he blows up Nerv and Tokyo-3. That scene in which Shinji destroys Nerv and Tokyo-3 is also a salute to the Evangelion fanfic Control, by claihm solais.

As of this moment, there are only three chapters left for Evangelion Gear, with one of them possibly being even longer than Episode 5. And in trademark Snafu fashion, there will be another twist that not you will not see coming.

Oh, and _**Bold Italic**_ Text denotes speaking German. There's a 'Kiss of the Dragon' reference and a 'Tekken' reference in the story somewhere.

Nerv Headquarters, the Geofront.

Gendou Rokubungi Ikari sat at his desk. Standing before him, was his Tactical Operations Director, Major Misato Katsuragi. But Gendou was not grilling Misato about the footage of her seen with Big Boss the day before. Instead, Gendou was on the phone with the United Nations' Secretary General (one of the few people who were not on Seele's payroll).

As it turned out, somehow, the confrontation between Big Boss and Commander Ikari had reached the Secretary General in Tokyo-2, and he was not very pleased.

Which is why Gendou was holding the phone away from his ear with his bandaged hand. Apparently, the shrapnel from the gun had cut him pretty deep, forcing Gendou to get stitches. Misato could hear from her place the Secretary General screaming bloody murder from the phone. It was a known fact that the Secretary General of the United Nations despised Ikari for his use of child soldiers in blatant disregard of the Valentine Treaty, but Gendou threatening a high-ranking General of the United Nations was the last straw.

Gendou knew that there were spies from the U.N. working at Nerv, but he dismissed them as a threat, seeing as how several of Seele's council sat on the Security Council. But now, he had the Secretary General on the line, trying to bite his head off. Misato looked on in slight amusement as the indomitable Commander Ikari was getting read the riot act. Normally, he would let Fuyutsuki deal with the rank-and-file, but the Secretary General was adamant. Either he speaks to Ikari himself, or he would be on the next train from Tokyo-2 to the Geofront...with an armed convoy.

The call concluded with the Secretary General threatening to send Gendou to the firing squad himself should he ever threaten a senior officer of the United Nations.

Gendou placed the phone back on the cradle. Assuming his trademark sinister pose, he turned to Misato. The young major looked back at the supreme commander of Nerv wondering how anyone could be intimidated by this man. She had seen the footage of Gendou threatening General Hayter with death should he continue to mentor Shinji.

Then came Hayter's response.

Misato watched as the old man had brutally, yet professionally took down six men. Six highly-trained men each one of them veterans of the wars that had followed after Second Impact, and their training and combat skills paled in comparison to that of the silver-haired, one-eyed general.

Misato suspected that there was more to the old man than it meets the eye.

"You wanted to see me, sir?" Misato asked.

"Yes, Major. You were seen in the company of General Hayter yesterday in Central Dogma. Explain," Gendou demanded calmly.

"He asked to be escorted out of the Geofront," Misato replied. "I would not dare refuse the order of a general."

"You also had a conversation with him. What about?"

"He asked me about my father. He had figured out that I was with the expedition to the South Pole."

Before Gendou could say anything else, he received another call from his secretary. "Commander, I got the Prime Minister on Line Two."

Gendou groaned. Threatening General Hayter turned out to be the worst thing he had ever done. He looked at Misato. "You may go."

Misato nodded and departed from the office, leaving Gendou to face the wrath of a equally pissed-off Prime Minister.

* * *

Central Dogma.

Major Katsuragi, and Doctors Akagi and Hunter were on the moving walkways that were used to get around the Headquarters. The topic of their conversation, Shinji's mentor.

"You must admit that the Commander made a big mistake in trying to intimidate not only a senior officer of the United Nations, but one who is a highly decorated war veteran," Naomi noted.

"A war veteran who took a apart six highly trained men," Ritsuko noted. At first glance, she had dismissed that the old man was a threat, but after seeing him not only subdue the six Section-2 agents with no trouble, but clearly intimidate Gendou Ikari with the threat of death, she realized that the old saying was true: appearances can be very deceiving.

"You met him beforehand," Ritsuko said. "What's your impression of General Hayter?"

"Like I said, he's pretty old-school," Misato replied. "But he's pretty wise. Given his age, he's been around since the Cold War. Maybe even got some classified missions under his belt. But I can say that the old man's been a good influence on Shinji. I really don't see why the commander sees him as a threat."

"Because Ikari wants someone that can be easily controlled," Naomi pointed out, speaking at Ritsuko's personal thoughts. "That is what it ultimately boils down to...control. But Shinji is a credible threat to his absolute control."

Ritsuko knew that it was true. Shinji was the only one who could pilot Unit One, and Gendou needed him alive in order to control Third Impact, as well as defend the Geofront when the time came for Seele to unleash their mass-produced EVAs. Too bad that unknown to Ritsuko, Misato and to the rest of Nerv, that little matter regarding both the nine EVAs as well as Tabris, were taken care of.

"I have to agree with Major Katsuragi," Naomi said. "The old man is quite the popular influence on young Ikari."

Ritsuko snorted. "Sure, you'd say that, since you're one of the few people who can talk to the kid without having him tell you to fuck off."

"Maybe it's because I don't treat him like dirt, despite the fact he has saved humanity many times over," Naomi replied calmly. "Regardless of everything, Shinji is still a kid."

The bottle blonde's next comment had all but died. Naomi had her dead to rights. Nearly everyone had treated Shinji like crap following his return from Unit One, herself included. Ritsuko's shoulders slumped as she dug into her pockets for a cigarette, only to find out she had none.

"If it wasn't for General Hayter, then Shinji would have killed himself," Misato said.

Both Naomi and Ritsuko looked at the ponytailed major in shock (well, for Ritsuko anyway).

"The old man told me himself," Misato continued. "Shinji stole my gun and had it with him during school. From what Hayter told me, he was originally planning on murdering Rei and Asuka, before deciding that he was only going to kill himself."

"Told you it was PTSD," Naomi said to Ritsuko.

"After meeting with Hayter, I started to look back at my own faults," Misato said. "Both as a person and as a guardian. I let my own obsession in getting revenge on the Angels override Shinji's well-being. I turned a blind eye to the abuse Asuka had put him through. We all did. And it nearly cost Shinji his life, as well as all of humanity...all because of our own selfish desires."

Naomi could relate to Misato. After all, her obsession with avenging both her adopted brother and her benefactor had been the driving point in her life. Until two years ago.

"You may be a medical officer, Ritsuko, but you're a scientist first," Naomi said.

Ritsuko's cellphone began to ring before she could reply to Naomi's comment. She retrieved it from her lab coat and answered it. "Doctor Akagi speaking."

"Sempai, it's Maya."

"What is it?"

"We got a big problem," Maya replied. "It's Unit Two. Come to the EVA Cages."

* * *

The EVA Cages, five minutes later.

Misato, Ritsuko, Naomi and Maya stood before Unit Two as it was shoulder-deep in LCL. Also present were Commander Ikari and Deputy Commander Fuyutsuki, both who had arrived minutes later.

"What's going on here?" Gendou demanded. "What is it that's so important to call the both of us out here?"

"We lost the core," Ritsuko said, directly to the point. "I don't know how but there was too much damage from the last battle. Unit Two is dead weight."

"Is there anything we can do?" Fuyutsuki asked.

Ritsuko shook her head. "You know as well as I do that once the EVA's core is destroyed, the EVA itself is useless, Professor."

"Hmm..." Gendou pondered this for a moment. "Send Unit Two to the EVA Graveyard in Terminal Dogma, Doctor. Also, prepare for a battery of tests for the Second Child in Units Zero and One. If she can't synch with either one of them, then there is no need for her to remain at Nerv." He raised his bandaged hand up, silencing Misato's protests. "She may be your ward, Major, but her gross insubordination following the last battle is something that I cannot and will not ignore."

'Hell, you ordered her to go after that strange mecha,' Misato thought darkly, remembering just how easily the mystery mecha handed Asuka's ass to her with drinks and a 'thank-you' card. 'Just like you to pass the blame onto someone else whenever you fuck up. This whole mess if your fault!'

Fuyutsuki's PDA began to ring. The old man answered it. "Fuyutsuki speaking." His eyes then went wide. "What...? Are you sure...?" Now his eyes narrowed. "Bring her to the Geofront immediately."

"Professor?" Gendou asked as Fuyutsuki ended the call.

"That was the Section 2 agents we had watching the school. Sohryuu's attacked both the First and Second Children, as well as assaulted several students. Both are okay, but Sohryuu's pretty banged up, thanks to Pilot Ikari."

"Have her taken to the detention cells while we sort out this matter," Gendou said. "This ends now."

* * *

About 30 minutes earlier, at Tokyo-3 Junior High School...

Upon arriving for class, Asuka did not receive the usual good mornings of her fellow admirers, but rather an ice-cold reception. The majority of the class was gathered around several laptops, Hikari, Touji and three others were gathered around Kensuke's laptop. Rei was at her desk, reading her textbook for the class.

"What's going on?" Asuka asked as she approached Kensuke's desk. "What the hell are you idiots showing Hikari?"

Kensuke's response was simple. He simply turned his laptop around to show Asuka herself.

Almost immediately, the color drained from Asuka's face as to what she was looking at.

The battle at the destroyed Matsushiro facility, complete with audio.

Bardiel - having possessed Touji's Unit Three - has just dispatched both Units Zero and Two, leaving Shinji in Unit One to face the possessed EVA.

"But...but I can't!" Shinji had objected to Gendou's orders. "I've got to save the pilot! I can't let them die! I can't kill a human being!"

"If you fail to fight, then you will die," Commander Ikari rebuked calmly.

"I don't care! It's better than having someone's blood on my hands!"

"I've had enough of this," Gendou had snapped. "Cut all synchronization between the pilot and Unit One."

"Cut it?" Asuka recognized the voice as that of Maya Ibuki.

"That is correct," Gendou's voice was as cold as ever. "Switch control to the Dummy System."

"But Commander, the Dummy Plug is still in its testing phase, and Doctor Akagi hasn't given her approval..."

Gendou cut Maya off. "It will be more useful than the pilot. Do it now."

As the video continued to play, Asuka knew that she was busted. Her deception was there for all to see.

"You...bitch," Touji snarled.

It was then, Asuka saw that the entire class (with the exception of Rei) has surrounded her.

Asuka gulped as she inched towards the open door. "L-look...I can explain everything...there's no need for violence, really," she said feebly.

"Get her!" one of the students shouted.

"Oh, scheisse," Asuka muttered as she took a page out of Shinji's playbook in dealing with people.

She ran for her life.

She ran, with the majority of the class chasing after her. Only Touji, Kensuke and Hikari remained behind.

"She lied to us..." Kensuke said. "All to stoke her own ego."

Hikari closed her eyes in shame. "I feel like such an asshole for trusting her," she said. "We believed her lies. We drove Shinji away."

"So...what do we do now?" Touji asked.

"We find Shinji..." Hikari said, "...and hope that he forgives us for how we treated him. Can't really blame him if he doesn't want to speak to any of us again, not after how we treated him."

"How?" Touji asked. "I thought he transferred out of the school."

The freckled class rep shook her pigtailed head. "He simply transferred to another class. Class 2-B. The rep there is a friend of mine."

"What about Asuka?" Kensuke asked.

"Let the others get their exercise," Hikari said flatly, not really caring whether or not the boys and girls chasing down Asuka break her legs.

From her desk, Rei Ayanami smiled as she continued to look out the window.

* * *

Lunchtime.

Rei found Shinji alone in Class 2-B, listening to his SDAT and eating his bento. For the past day, Rei had been working up the courage to confront Shinji and apologize for her actions. With Asuka being occupied with the irate students of Class 2-A regarding the incident at Matsushiro, she decided that now was the time to confront Ikari.

She just hoped that Shinji was willing to bury the proverbial hatchet with her, rather than IN her.

Rei approached Shinji, who continued to ignore her as he ate his lunch. "Pilot Ikari," she began.

Shinji said nothing as he continued to ignore her.

Rei decided to try again. "Pilot Ikari."

Again, Shinji decided to ignore her.

This time, Rei took action. Crouching down, she reached over and removed the ear buds from Shinji's ears. Before Shinji could respond Rei's actions, she did something he wasn't expecting.

She called him by his first name.

"Shinji."

That caught him off guard, if only for the moment.

"Shinji, please let me speak," Rei pleaded.

Shinji's face was that of surprise, but only temporary. He remembered Rei's response all too well following his return from Unit One's core. His face became unreadable, as it has been for the past month. "You got three minutes," he said.

Rei nodded. "Shinji...I am sorry for how I reacted following your return from Unit One's core. I was acting on what Commander Ikari had told me. He told me lies about what had happened at Matsushiro, and I believed him. I found out the truth, just recently, by looking at the video archives. Commander Ikari had used the Dummy System with my imprints to control Unit One. What had happened to Suzuhara was not your fault. The blame lies entirely with him."

"You, out of all people, condemning him? The last time I criticized the old bastard, you slapped me."

"And I also apologize for that as well. In the past month, I have seen things with a clarity that I have not seen before," Rei admitted. "I can see why you despise him, Shinji. As for Sohryuu...let's just say that as of right now, she is receiving her comeuppance." Off Shinji's slightly confused look, Rei simply said, "I simply leaked the video of what had happened at Matsushiro to the class." She gave him a small smile. "Suffice to say, the results were not very pleasant for Sohryuu. Last I saw of them they were chasing her through the gym. Although I am rather curious how they managed to produce torches and pitchforks on such short notice."

Shinji was touched by the gesture. "You did all of that...for me?"

Rei nodded. "I wish to try and mend the bridges between us. And by exposing Sohryuu as the fraud she truly is, I hope that we can once again be friends."

Shinji thought about that for a long moment. For the longest, he had tried to break through Ayanami's shell. The smile she had given him during the Yashima Operation proved that. But Ikari saw that Shinji was a threat to Rei and moved against him while he was inside the EVA's core, by giving her a slightly altered chain of events following the Matsushiro incident.

Thankfully, Gendou did not notice her snooping around, otherwise, he would quickly have her replaced.

After thinking it over, Shinji made his decision. "Okay...I'll tell you what. You start from one end, and I'll start from the other. We'll meet in the middle."

Rei smiled. "I would like that, Shinji."

Voices were heard from outside, as the classroom door slid open, and Hikari Horaki, Kensuke Aida and Touji Suzuhara entered. Almost immediately, Shinji was on his guard as he stood up from his desk, ready for anything. Not that the crippled jock, the otaku and the pigtailed class rep were a threat.

The three students bowed in unison to their former classmate. "Shinji Ikari," Hikari began. "We apologize for our actions this past month towards you. Asuka has deceived us. All of us." They re-assumed a vertical position, as Hikari continued to play the role of peacemaker, while Kensuke filmed the events. "We found out the truth about what had happened to Touji. There is no excuse for what Asuka had done."

Before Shinji could reply to his former class rep's apology attempt, the door slid open and Asuka Sohryuu came running inside the classroom, slamming the door behind her, ducking behind said door as the virtual lynch mob came running past her hiding spot.

Once they were gone, the halvsie German turned and saw that she was in the classroom with the one person she had grown to clearly despise.

Almost rapidly, Asuka's expression changed from to being scared to being pissed.

That was when all Hell had broken loose.

Asuka screamed as she charged towards Shinji, knocking aside Hikari, followed by Touji when he tried to come to her aid. Kensuke got out of the way, the camcorder glued to his face as he filmed Asuka charging at Shinji, screaming bloody murder, fists raised to deliver serious pain...

...only to see Asuka's face come into contact with Shinji's foot, the end result of another boot-to-da-head. Asuka landed on her ass in an undignified heap.

"You just don't learn, do you, Sohryuu?" Shinji taunted as he went into his CQC stance. "Fine. I'll oblige you yet again."

"You...YOU FUCKING BASTARD!" Asuka screamed. "I'LL FUCKING KILL YOU!"

Shinji ducked under Asuka's wild punches and quickly countered with a uppercut with his right hand, nailing Asuka on the kisser, followed by a hard left elbow to the side of Asuka's face, drawing blood from above her eyebrow. Rei, in the meantime, had quickly produced her cellphone and had Section 2 on the line.

Asuka countered by nailing a punch to Shinji's head, causing him to stumble back slightly, allowing Asuka to grab a nearby desk. Pushing it towards the Third Child, in an attempt to trap him in between her desk and the one behind him, Asuka thought she had Shinji cornered.

But once again, Shinji surprised her.

Shinji quickly shook off Asuka's punch, and saw her pushing the desk towards him. As Touji, Kensuke, and Hikari watched in complete surprise, Shinji performed a suicide kip-up. Otherwise known as a Chinese kip-up, Shinji hopped backwards, landing on his shoulders, just as Asuka slammed the desk into the spot he was at moments earlier. Pushing himself off the desk with his hands and shoulders, using the thrust's momentum to carry his body feet-first, arching his back as he pushed himself upwards into a squatting position, right before kicking Asuka square in the face yet again.

It was clear that by the look that Asuka was giving to Shinji that the German redhead had clearly snapped.

'KillkillkillKILLKILLKILL!' Asuka's mind chanted as she lunged at Shinji yet again...only to be slammed to the ground yet again.

Hikari, Touji, and Kensuke watched in utter amazement as Shinji Ikari brutally countered Asuka's attacks, each time, throwing or slamming her to the floor, schooling the redhead in the art of CQC. But Asuka merely shrugged it off in her rage. Ever since Shinji had reached 400 percent during the battle with Zeruel, Asuka's opinion of him had lowered drastically, which led her to plot against the Third Child, in an attempt to get her synch ratio back to the number one spot.

With her scheme exposed, not to mention the humiliating defeat following the Angel battle at the hands of the mystery mecha, as well as the fact that Shinji Ikari - a person who she saw as inferior to her - was clearly better than her, given his kill record, Asuka Sohryuu sought to remove the one person that was the obstacle to her greatness.

Shinji Ikari.

Shinji blocked Asuka's wild swings with his forearms. When Asuka lunged again, Shinji responded by grabbing her wrist and yanking her forward, causing his opponent to go off balance. Asuka felt her head jerk forward violently as she felt Shinji's foot collide with the back of her head, right before seeing him snap the same leg back, striking her in the face, knocking her down, crashing into several more desks as she fell to the ground.

But before Asuka could attack again, two burly Section 2 agents charged in and quickly took down Asuka, followed by the female agent Gendou ordered to tail Shinji.

"NOOO!" Asuka screamed. "LET ME GO! LET ME GO!" To Shinji, she yelled, "THIS ISN'T OVER, IKARI! I SWEAR TO GOD I'LL KILL YOU FOR RUINING MY LIFE!"

The two agent dragged Asuka out, the redhead kicking and screaming in Japanese and German. Meanwhile, the female agent noticed Kensuke and his videocamera. Walking over to the bespectacled military otaku, she extended her hand out.

"The memory card, please," she asked politely.

Kensuke complied, not wanting to be on Section 2's shit list again. That one time while Shinji was fighting Shamasel was bad enough. He handed over the card and after taking the statements from all those involved, she got on the horn with Deputy Commander Fuyutsuki.

"Fuyutsuki speaking."

"Sir, Pilot Sohryuu has attacked Pilots Ikari and Ayanami, and has assaulted two civilians."

"What...? Are you sure...?"

"We have the First and Third Children's statements, as well as those of the civilians and video evidence of the attack."

"Bring her to the Geofront immediately."

"Right away, sir."

* * *

The Geofront, Nerv Headquarters, several hours later.

Supreme Commander Gendou Ikari read the reports that were filed by Section 2, as well as viewing the confiscated footage from the otaku's camcorder. Flanking him on either side, were Deputy Commander Fuyutsuki, Doctors Akagi and Hunter, Ryouji Kaji (who had been called in, given his position as Asuka's former guardian), and Major Katsuragi. And aside from Gendou Ikari, none of them looked very happy.

Truth be told, Gendou could care less about Shinji. The boy already had his balls in a vice grip. But Asuka had tried to attack Rei, and that he found intolerable. And given the fact that Unit Two was dead weight and was on its way to the EVA Graveyard, there really was no point in allowing Asuka to hang around any longer.

The cause of their anger was in a chair in front of them, once again battered and bruised, flanked by two Section-2 agents. For most of the day, Asuka sat in a holding cell, while the senior Nerv hierarchy pondered her fate. With the evidence in front of them, it was clear for all of them.

Now, it was time to lower the boom on the renegade pilot.

Gendou closed the file and assumed his sinister pose. "Asuka Langley Sohryuu, given the reports I have seen, and the testimonies from the witnesses at the high school, as well as your past history with both Pilots Ikari and Ayanami, you are a serious liability to Nerv. Nerv exists solely to defend humanity from the Angels and to prevent a Third Impact, not to stoke anyone's ego, especially your own. Do you have anything to say in your defense before I pass judgment?"

"..." Asuka was silent, glaring daggers at the Nerv Supreme Commander.

"Pilot Sohryuu, you have been found guilty of attempted assault on Pilots Shinji Ikari and Rei Ayanami, as well as the charges of assault on a civilian. You have also violated the restraining order placed on you by Pilot Ikari. Your actions have brought disgrace not only upon yourself, but also upon Nerv. And given the fact that Unit Two will no longer work, since the core is now useless, there is really no need for you to remain here. Your employment with Nerv has been terminated effective immediately, your pilot status has been officially revoked, and you have been officially disavowed."

"WHAT?" Asuka screamed as she attempted to lunge at Gendou, but was quickly restrained by the two agents. "YOU CAN'T DO THIS TO ME, YOU BEARDED BASTARD! I'M THE BEST PILOT YOU HAVE IN THIS GODFORSAKEN HELLHOLE! ME! ONLY ME! THAT BAKA SON OF YOURS AND THAT BLUE-HAIRED WONDERSLUT ARE NOTHING COMPARED TO ME! NONE OF YOU ARE! ALL ARE YOU ARE BENEATH ME! FUCK YOU! FUCK ALL OF YOU! ALL OF YOU ARE BENEATH ME! YOU'LL GET YOURS! ALL OF YOU!"

Asuka was quickly silenced when one of the two Section-2 agents produced a stun gun and shocked Asuka into silence.

To the agent wielding the stun gun, the supreme commander said, "Thank you." He then continued with his judgment. "You will be taken to New Narita Airport under guard and placed on a flight back to Berlin," Gendou continued. "Your belongings have been removed from Major Katsuragi's apartment and incinerated. Should you breathe a word to anyone about your time here at Nerv, you will be spending the next twenty years inside a maximum-security prison."

To the two Section-2 agents, he made a simple hand gesture and the two men in black hauled Asuka to her feet and dragged her out of the office.

The last thing Asuka had said as she was dragged out of the office was, "Damn you...goddamn you...all of you."

"This matter is now closed," Gendou said. "All of you are dismissed."

* * *

Central Dogma.

Once the gathered senior Nerv members went their separate ways, Misato caught up with Kaji. Before the ponytailed man could say anything, Misato had beaten him to it.

"Take me to Shinji."

Much to her surprise, Kaji had accepted her request. "I'm heading there now to check up on him. Come with me."

* * *

En route to Shinji's apartment, Misato looked out the window, while Kaji was behind the wheel of the Nerv-owned sedan. The events that had happened earlier that day still weighed heavily on her mind.

"Something on your mind, Misato?" Kaji asked.

"Am I a good person?" Misato asked.

"What do you mean?"

"I may be a competent tactical officer, but when it comes to playing guardian, I failed," Misato lamented. "Shinji's gone...Asuka's a certified sociopath...damn it...we were a family. Where did it all go wrong?"

"Nobody's perfect Misato," Kaji offered. "Look at how Asuka was raised. Her mom committed suicide after losing her mind in Unit Two, her father and stepmother want nothing to do with her, and she was basically groomed to pilot EVA and nothing else. Nerv-Germany had seen the signs of Asuka's disorder, but did nothing to help her. Instead, they simply swept it under the rug and stoked her ego."

Misato wasn't convinced. "Maybe..."

"Look on the bright side, at least you still got a chance with Shinji," Kaji pointed out. "You shouldn't worry about him. I heard from the old man from what Shinji was planning to do with Sohryuu and Ayanami. Good thing he didn't go through with it."

"You knew?"

"I should. Big Boss himself told me."

Misato blinked. "Big Boss? You mean the legendary soldier himself? That Big Boss? What does he have to do with this?"

"Easy," Kaji said, flashing her his grin. "General Hayter **is** Big Boss."

Misato looked like she was gut punched General Hayter was the legendary mercenary himself? Then she palmed her face. 'Of course!' she berated herself. 'Only Big Boss knows that style of CQC! And he taught it to Shinji!'

Shortly before her assignment to Nerv Headquarters, she had heard about the declassified reports on Operation Snake Eater, as well as the pardons for The Boss, Big Boss' former mentor and Big Boss himself. Of course, like everyone else, she thought the old man had died in Zanzibarland the year before Second Impact. He is basically a virtual legend to the military and espionage community.

"Of course, the old man was concerned whether or not you were a agent of Seele," Kaji said "But I vouched for you. After all, why survive Second Impact at Ground Zero and work with Seele to unleash Third Impact?"

Misato frowned. "Wait...you're working for Big Boss?"

Kaji nodded. "Yup. He saved my life when I was a kid. I never told anyone about this, not even you. Second Impact was hell despite the fact that Japan had weathered the storm nearly intact. But Japan still had to deal with the fallout of the Impact. My parents had died following Second Impact when Japan was ravaged by the earthquakes that nearly destroyed the country, and the riots that followed, forcing the Japanese government to declare martial law, leaving myself and my brother alone, no family or friends. We fell in with a group of orphaned children and stole food to survive."

His expression grew somber. "One night, it was my turn to go and steal some food. I snuck into a JSDF base, but I got caught. The soldiers threatened to kill me unless I told them...told them where my brother and the others were hiding." His hands tightened on the steering wheel. "I was scared of dying...so I chose to betray my friends...and my brother. The soldiers gunned them down, before turning their guns on me, having no intention of honoring our deal. Big Boss appeared and saved my skin. He found me crying, cradling the body of my dead brother. He took me to an orphanage, when I remained until I was 17. Two years ago, he found me and proposed that I work for him. I agreed, since I owed him my life."

"Ryouji...I...why didn't you tell me?" Misato asked.

"Same reasons why you never talked about your dad," Kaji replied.

The ride to Shinji's apartment continued on in silence.

* * *

Shinji Ikari's apartment.

Lying in his bed, with his SDAT playing Beethoven's Fifth Symphony, hands behind his head, Shinji stared at the ceiling. He had plenty of time to think about what has happened to him in the past month. More importantly, he was thinking about the incident with Asuka at the school. Naomi had sent him a message notifying him of Asuka's sentence, and was actually glad that the old bastard finally did something right.

But more importantly, Asuka's deception had been finally revealed, thanks to Rei. On top of that, he had forgiven Hikari, Touji and Kensuke, but it would take a while for them to become friends again. The wounds were too deep. They would have to earn back his trust. Shinji wasn't going to just jump back into things like before. That was the old him. He would never go back to how things were - being pushed around and treated like dirt. Those days were over.

Surprisingly enough, Shinji felt no remorse over Asuka's fate. It was then, Big Boss' words came back to him regarding his former friend.

_'Even with so much bad blood between us...it's actually kind of funny. The hatred is gone. All I feel is a deep sense of longing. And pity. Even after all this time, I still wonder...did Zero really hate me? Or did he fear me?_'

'Was it the same between me and Asuka?' Shinji wondered. 'Maybe through her oversized ego...did she fear me...or did she hate me...?'

As the SDAT began to rewind the tape, Shinji heard a knock on the door. He looked at the clock on the nightstand. It was nearly 11 p.m. Big Boss wasn't the one to visit so late. Rei would be at home.

That left Kaji.

Shinji clicked off the SDAT and got out of the bed. Walking barefoot across the hardwood floor, he stopped at the door, unlocked it, and opened it.

Standing on the other side, was Ryouji Kaji and Misato Katsuragi.

Before Shinji could say something, Misato quickly cut him off. "Shinji, we need to talk."

Shinji stood his ground in the doorway. "So talk."

Kaji stood to the side, as the former guardian faced her former ward. "Shinji...I honestly did not know how you felt about piloting the EVA. Nor did I notice how Asuka acted towards you. I was simply blinded by my own desires for vengeance. I guess it took Big Boss to see it from a different point of view."

That caught Shinji's attention. "You talked with Big Boss?"

Misato nodded. "Yeah. The man's practically a living legend. Your father even spoke with him."

Shinji's eyes narrowed. "That bearded bastard is not my father. And what did he want with the old man?"

"Tried to intimidate him," Misato said. "Big Boss ended up sending six Section 2 agents to the medical ward, shot Gendou's gun from his hand and made said bearded bastard piss himself."

That made Shinji crack a smile. He had wondered what had gotten the old fart and Ritsuko spooked the last time he saw them. Big Boss had that way with people.

Misato returned the smile, albeit it was a sad one. "You don't have to worry about Asuka anymore. She has been officially stripped of her duties as an EVA pilot and sent back to Germany in disgrace. Rei explained to me that she turned the class against you with her claims about what had happened at Matsushiro. I really don't blame you for moving out and transferring to another class, Shinji. But I would like for us to be friends once again."

Shinji said nothing after Misato's apology. After a moment, he slowly extended his hand out. Misato saw that as a start, as she shook Shinji's hand, the handshake speaking more than Shinji ever could.

Maybe the bridge between her and Shinji could be repaired after all.

* * *

Katsuragi Asylum, the following morning.

Misato's cellphone rang as she sat down with her can of beer. Looking at the caller ID, she saw that it was Fuyutsuki, since Gendou had no reason to call her, leaving the Deputy Commander to handle the day-to-day affairs of Nerv.

Misato flipped the phone open and answered. "Major Katsuragi speaking."

"Major, it's Fuyutsuki," the old voice of Nerv's second-in-command replied. "We have a problem."

"What is it, sir?"

"Sohryuu has gone missing."

Misato's eyes went wide. "What?"

"Sohryuu was supposed to switch planes once she arrived in Nagasaki, but she has vanished," Fuyutsuki explained. "Her Section-2 detail has been found slaughtered. I have already alerted the other branches all over the world, but it's as she had vanished from the map."

"This is bad, sir," Misato said.

"On that I agree."

"Do you think she killed the guards that were with her?"

"Not likely. The detail assigned to her were war veterans. Something is amiss. I will keep you informed if anything comes to light, Major."

"Thank you, sir."

* * *

Location - unknown, hours later.

Two FROGS ushered in a bound girl, her face covered with a dark shroud. The two heavily-armed soldiers placed their 'guest' into a chair, and removed the shroud, revealing the woman to be Asuka Sohryuu.

Standing behind the woman, they ignored the disgraced Evangelion pilot as she shouted threats and curses to them in German. Then she stopped when she heard an old man's voice, speaking to her in German.

"To have given so much to Nerv, only to be thrown away like garbage...my poor, poor child."

"What? Who are you? Who's there?" Asuka demanded, also speaking in German.

Her question was answered when strobe lights came on, illuminating something she recognized instantly. A production-model Evangelion. Unlike her Unit Two, the color scheme was reversed - black with red trim.

A second light came on, bathing the owner of the voice in its light.

An old man dressed in robes, a visor over his eyes, and short white hair. A hologram of Zero.

"_**You can say that I am one of your admirers, young Sohryuu,**_" Zero said, returning to his Keel persona. He made a gesture and one of the FROGS undone Asuka's bounds. "_**I've brought you here for one purpose, Sohryuu. To make you an offer.**_"

Asuka looked at the Evangelion, then back at Zero. "_**I'm listening.**_"

Zero smiled. He had read Sohryuu's psych files, and given her obsession of becoming number one by any means possible, manipulating her would be easy. Too easy.

"_**This is Unit Five, advanced prototype of the production series,**_" the old man explained. "_**Unlike your Unit Two, this one has a working Super Solenoid core, which makes internal batteries and power cords unnecessary. I have chosen you, Asuka Sohryuu, to pilot it.**_"

"_**What's in it for me, old man?**_"

"That's simple. Revenge against those that betrayed you, those who failed to see your true potential. Join me, Sohryuu, and I will grant you your revenge."

Given her advanced intelligence, Asuka should have refused. But her ego demanded stroking, not to mention that the idea of taking revenge on Nerv - their pilots in particular - was very tempting.

"_**You got yourself a deal, old man,**_" Asuka said.

"**_Good. Very Good. Let's begin your advanced EVA training._**"

Asuka smiled evilly. 'Soon, Shinji...you'll be seeing me again very soon...'

**OMAKE!**

What if Big Boss did not show up at the park?

Inside a secluded section of the city's park, Shinji Ikari sat on a bench, alone. To say that he was depressed was a total understatement.

Given the fact that he currently had Misato's service pistol in his hands, having pilfered it earlier from her belongings earlier that day, it was clear that he was suicidal.

It had started following Zeruel's attack on the Geofront. Never mind the fact that he had just saved everyone from Third Impact for the seventh time. He was still treated like dirt by Asuka (who had destroyed his cello, saying that she was bored) and snubbed by Ritsuko. Even more worse, Touji and his family blamed him for what had happened with Zeruel. Not that Shinji could do anything about that, since it was his bastard of a father that had used the Dummy Plug and had nearly killed Touji. Even worse, Asuka had told everyone in class that it was Shinji's Unit One that had crippled Touji, effectively turning everyone against Shinji, while painting herself as the valiant heroine. Even Kensuke had turned his back on him.

But what hurt the most was Rei's reaction, following his return from the EVA's core, despite the fact that he had saved her life.

She had said only one word to him, after she had slapped him.

Coward.

Which is what led Shinji to where he was at now. Earlier that morning he had snuck into Misato's bedroom and had stolen her pistol while she slept in an alcohol-induced stupor. It was loaded, as it had always been. He made it through school, ignoring Asuka's heckling and the whispers and insults of the other classmates, all the while Misato's pistol was in his backpack, within distance. He wondered how many he could kill before turning the gun on himself.

He came close to revealing the pistol and putting a slug in Asuka's head, as well as Rei's. But he relented. Once school let out, he did not go back home. There were no synch tests to be done, so Shinji decided to head for the park.

Looking down at the pistol, he slid the slide back, making sure that a round was jacked into the chamber before snapping the slide shut.

'One bullet,' he thought. 'One bullet is all I need. It will be over. All over.'

Shinji flipped the safety off. After a moment, he closed his eyes and raised the gun to his head.

**BLAM!**

The birds scattered to the skies upon hearing the single gunshot.

* * *

Tokyo-3 Junior High School, the following day.

Asuka Sohryuu noticed that Shinji had not returned home the previous night, as did Misato. However, as Asuka had entered the school grounds, Misato was at the scene of the suicide, where she had identified Shinji's body...as well as recognizing her gun which Shinji used to take his life.

Rei Ayanami was waiting for her as she stepped into the classroom, with Hikari. She stood up, and confronted the German redhead. "Sohryuu...do you know where Ikari is today?" she asked, her normally monotone voice laced with pure venom.

"Like I give a damn about that spineless baka," Asuka snorted. "The coward failed to come home last night. I hope the jerk is dead!"

**WHAM!**

Asuka did not see Rei's incoming fist until it was too late. It was a full-body swing too; came out of Terminal Dogma, where she spent most of her childhood, and it picked up speed through the halls of Central Dogma, then hooked a right through the streets of Tokyo-3, where it crashed into the jaw of the Second Child, sending her to the floor.

The entire class went silent. Rei Ayanami has just decked Asuka Sohryuu.

Before Hikari could reprimand Rei for punching her friend, Rei spoke in a cold voice.

"You have been granted your wish, Sohryuu. They found his body in the park 20 minutes ago. Self-inflicted gunshot wound to the head."

The entire class fell silent. Shinji Ikari had committed suicide. And they all had a hand in it, driving him to the brink of madness, following Asuka's every word.

"I received the call from Deputy Commander Fuyutsuki," Rei snarled. "I hope you're proud of yourself, Sohryuu. We drove an innocent to death."

With that said, Rei stalked past the redhead, who was still holding her jaw, leaving all of Class 2-A in shock. Shock then changed to guilt, an overbearing guilt that the entire class had shared, once Kensuke used his camera to verify the news.

Shinji Ikari was dead.

To Nerv, their top pilot dead meant a lot of trouble.

* * *

The funeral of Shinji Ikari was held several days later. With the exception of Asuka and Gendou, Class 2-A and the senior members of Nerv were present. Both Asuka and Gendou were absent, but for different reasons.

Rei had released the video of what had happened at the destroyed Matsushiro facility to Class 2-A, which led to Asuka running for her life from the virtual lynch mob that consisted of not only Class 2-A, but the entire school. She remained behind at the Katsuragi Asylum for her own safety, under armed guard lest her former classmates tear her apart.

Gendou, on the other hand, was dead. His initial response in regards to his estranged son's suicide were indeed callous, showing absolutely no remorse or any kind of emotion for his son's suicide. That led to Ritsuko gunning him down in the bowels of Terminal Dogma. Once Gendou was dead, she attended the funeral alongside the other Nerv members.

Misato had found out the role Asuka had played in Shinji's suicide and was enraged, as was the newly-appointed Commander Fuyutsuki. She was stripped of her duties as a Nerv pilot and sent back to Germany. With the loss of their best pilot, and Asuka being sent home in disgrace, only Rei remained behind. Even worse, the Dummy System had been rejected by Units One and Two.

Once again, the world was screwed.


	8. Episode 7: The Beginning of the End

_**Episode 7: The Beginning of the End**_

Snafu's Notes: Yes, I plan on making Asuka one of the major villains in the story, given her allegiance to Zero, thus setting up for an epic showdown with Shinji in Tokyo-3. Also, I've also taken another slight deviation from the NGE storyline (not that anyone has been complaining, given the positive reviews I've been getting, despite killing off Tabris and destroying the mass-produced EVAs).

For the battle against Armisael, it is not in the Tokyo-3 area, but rather at the Matsushiro ruins, solely because for the next chapter, I want Tokyo-3 to be left intact for the upcoming battle. Also, in the Evangelion storyline, Ritsuko knows about her mother's relationship with Gendou. But what if the bottle blonde mad scientist DID NOT know about Naoko's sexual liaisons with the Bastard King of Nerv? How will that play out?

For those who are stumped about the Tekken reference, it's the double boot-to-da-head that Shinji uses on Asuka, which is one of Kazuya's throws.

Following the encounter with General Hayter days earlier, Ritsuko's curiosity was piqued. Misato spoke highly of him. Shinji had learned how to fight because of him, and held him in high regard. And Gendou was scared of him, given the fact that he pissed his pants in front of herself and Fuyutsuki.

She was inside her office, seated in front of her laptop, lit cigarette dangling from her lips, cup of lukewarm coffee resting nearby, untouched. Using the MAGI, she had hit pay-dirt. Using the MAGI, she had hacked into the U.S. Army database.

The bottle blonde mad scientist scrolled down the list of Special Forces, until she came across one that looked very peculiar.

The insignia was that of a fox holding a knife by the handle in its mouth. The name of the unit, was FOXHOUND.

"Hmm...High-Tech Special Forces unit, codenamed FOXHOUND," Ritsuko read. "An elite black ops unit established by Big Boss in 1971. FOXHOUND specializes in covert solo infiltrations, to cope with local revolutions, regional complications and global terrorist activities in unauthorized combat zones that are politically sensitive to intervene through conventional means. There were four primary groups within FOXHOUND - The Sneaking Unit, The Spy Unit, The Tech Unit, and the Medical Unit."

Taking another sip of her coffee, Ritsuko continued to look through the files. "The Sneaking Unit has four four-man units - Alpha, Bravo, Charlie, and Delta teams, who specialized in infiltration missions as well as abducting and/or rescuing potential recruits. The Spy Unit's specialty is espionage missions into enemy territory, as well as transporting intel on events that could be exploited to the unit's advantage. The largest of the unit, with eighteen four-man units in total. The Tech Unit's specialty is the development of new technologies and weapons. And the Medical Unit was responsible for tending to the soldiers wounded in battle."

Curious, Ritsuko pulled up the file on the unit's founder...

...and her cigarette dropped into her coffee cup, where it fizzed out upon impact, as Ritsuko's jaw was opened in total shock.

The combed back white hair. The trimmed beard. The eyepatch over his right eye. The thousand-yard stare.

General John Hayter **is** Big Boss.

Suspecting that the dossier that she had found was a doctored copy, Ritsuko punched in several keys on the laptop. Seconds later, Big Boss' dossier came up.

Most of it was on the dossier that she had given to Gendou, but this one went into further detail. Every single black-op, assignment and mission from the Cold War to pre-Second Impact.

Ritsuko thought of only one thing. 'Holy shit.'

"Doctor Akagi."

Naomi's voice snapped Ritsuko out of reading Big Boss' dossier. She looked up, and saw the resident junior medical officer/senior psychologist standing in front of her desk inside her dark office. "Oh...it's you, Doctor Hunter," Ritsuko said. "What is it?"

Naomi waved the folder in her hand. "I got the psych evaluation for Shinji Ikari, as per Commander Ikari's request." She set the folder down and started to leave, but stopped and turned around. "Actually, there is something else, Ritsuko," she said. "You nearly jumped out of your seat when I called you." She began to circle around the desk, slowly. "Which means, you were doing something very naughty."

"Umm...it's nothing, really," Ritsuko said, all of a sudden Nervous around the older woman. "Just running a performance check on the MAGI, that's all."

Naomi cocked an eyebrow. "From your personal laptop?" she asked as she reached out, and turned the laptop around, so that she was looking at Big Boss' dossier. "You're a lousy liar, Akagi. I thought you would be at least satisfied with that little dossier I created, just in case Gendou would come snooping around. As expected, he took the bait."

Ritsuko's eyes widened in realization. "You...you're working with Big Boss?"

"Yes," Naomi admitted. "I know the old man very well. Twenty years ago, after my parents were killed in the Rhodesian Civil War, he helped me and my adopted brother gain entry into the United States. Prior to the Shadow Moses Incident nine years earlier, I was the chief medical officer of FOXHOUND."

She looked at the photo of Big Boss and smiled. "He is my benefactor. A father figure to me. A secret well-kept. It was through his connections that I was recruited into Nerv's American branch. It was only a matter of time before I was assigned here, as a mole, to keep an eye on things."

Naomi tapped at the laptop. "You know...a secret like this can be very dangerous if exposed. I've personally hid this file for a reason," she said.

Ritsuko gulped.

"But you just kept on digging. You wasn't satisfied with the altered file." She sighed. "Oh well. Consider yourself lucky that Big Boss wishes to have a word with you."

"What?"

That was all Ritsuko said before she felt something prick her neck. Suffice to say, she was unconscious before her head hit the desk.

Stepping out of the shadows, dressed in a Nerv worker's uniform, complete with OctoCamo to give her face Japanese features, was Laughing Octopus. In one hand, she held a syringe which contained the knockout serum.

Octopus handed Naomi a spare facial OctoCamo. "You have your orders from the old man," she said. "I'll take care of things here."

Naomi nodded as she opened her lab coat, showing that she was dressed in the same clothing as Ritsuko. slipping the camo over her head, she activated it, thus taking on Ritsuko's likeness. A small digital strip on her throat allowed her to speak in Ritsuko's voice as well. Naomi retrieved Ritsuko's ID and after pocketing her own ID, snapped Ritsuko's ID on her jacket.

Naomi's next stop, was Terminal Dogma.

* * *

Nerv Headquarters, Level EEE - Terminal Dogma.

Sneaking into Terminal Dogma was easy enough. Thanks to Otacon and Mei Ling, Naomi had a thirty-minute window to perform her task before Gendou found out that something was amiss.

Still wearing the OctoCamo with Ritsuko's face, Naomi stood before the Reiquarium, where numerous copies of Rei Ayanami floated in a massive tank of LCL. Naomi stood transfixed for a moment, watching the copies of the blue-haired pilot, their red eyes watching her.

It was apparent that Zero had given the key aspects of the Les Enfant Terrible project to Gendou, allowing him to create the perfect pilot, using 1 percent of Yui Ikari's DNA (for her facial features), 98 percent of an unknown woman's DNA, and 1 percent of Lilith's DNA.

It was ordered by Big Boss to sabotage Nerv in any way, shape, form and fashion. Naomi had told him about Rei's origins, as well as the Reiquarium inside Terminal Dogma. His orders were swift: sabotage the Reiquarium, and bring Ritsuko Akagi in for questioning. While the unconscious Ritsuko was being loaded into a Nerv supply truck and taken to the JSSDF Base Haruna, Naomi was typing away at the console.

After a few seconds, Naomi hit Enter, turned on her heel, and left the room, as the LCL's color changed from orange to blue, the spare bodies inside the Reiquarium began to dissolve and break apart in the midst of their robotic laughter. To make sure that they would not be used again, Naomi drew out a small revolver and unloaded six rounds into the console. A small pack of C4, set to detonate after she had made her escape, will take care of the Dummy System. She made sure that the security cameras would see her - or rather, Ritsuko - leave Terminal Dogma.

* * *

About 30 minutes later...

Gendou stood in front of the LCL tank that was formerly the Reiquarium. The remains of the Rei clones rested at the bottom of the tank. Fuyutsuki stood beside him. The younger man was trembling with rage as Fuyutsuki gave his report.

"I had Section 2 check the video survailiance," the old Deputy Commander reported.

"And...?" Gendou said through clenched teeth, incredibly furious that his scenario had once again been diverted.

"It was Ritsuko."

Gendou slowly absorbed the news with surprising calm. Inside, he was furious at this betrayal. "Professor...I want Akagi found...now."

Fuyutsuki recognized that tone anywhere. With the Reiquarim and the Dummy System destroyed, the bottle blonde had all but signed her death sentence. The old man hoped and prayed that Ritsuko found herself a nice little hole to hide in until the conclusion of the war.

* * *

JSSDF Base Haruna, outside of Tokyo-3.

An interrogation room.

Ritsuko Akagi saw in a chair, handcuffed, head slumped forward, showing that she was still unconscious.

An hour earlier, Laughing Octopus had piled Ritsuko's unconscious form - which was hidden inside a crate - into a Nerv supply truck - which had been driven by Revolver Ocelot, also in disguise - where it was taken out of the Geofront and driven towards the JSSDF Base Haruna.

Seated across from her, was Big Boss, the table the only thing between them, the only item resting was a pack of cigarettes and a lighter. Rather than the formal uniform he wore when he visited the Geofront, he was instead dressed in camo fatigues - tiger stripe, the main uniform of FOXHOUND (i.e. think his Tiger Stripe camo from Snake Eater, minus the heavy utility belt), showing that he had been conducting war games with FOXHOUND and the JSSDF.

The old man reached into his pocket and pulled out some smelling salts. Within seconds, Ritsuko was back to full consciousness. One her vision cleared, she found herself looking at the one-eyed soldier who had made such an impact in both Gendou and Shinji's lives.

"Doctor Ritsuko Akagi. How nice of you to join us," Big Boss drawled.

"You...you..." Ritsuko sputtered.

Big Boss cut her off as he stood up and undone her bounds. "It was either us or Seele. They had a squad waiting for you when you arrived at your home. At the moment, my colleague is 'interrogating' them for information, leaving me with you. You can calm down, Doctor. If I wanted you dead, I would have killed you inside the Geofront. I had you brought here to answer some questions I have in regards to Nerv."

It was at that moment, the door opened and another person stepped inside. Ritsuko's eyes bulged out of her head as she found herself looking at her own doppelganger.

"It's done, Boss," 'Ritsuko' said. "The Reiquarium has been destroyed."

Big Boss enjoyed the look on the real Ritsuko's face. "I'm willing to bet that Gendou or Seele would kill each other to get their hands on our technology," he said as the false Ritsuko's face vanished, the woman revealing herself to be Naomi Hunter once the OctoCamo was removed.

"As we speak, Gendou has Section 2 scouring Tokyo-3 for you," Naomi explained. "And Seele is also looking for you, as they believe you killed the team sent to kidnap you. Both have termination orders. You're not exactly popular at the moment, Ritsuko."

"Which is why we decided to intercept you before Seele or Section 2 did you in," Big Boss said. "Abduction is a classic FOXHOUND specialty."

"I know. I read the file," Ritsuko said, still Nervous.

Big Boss turned to Naomi. "You can go. Return to the Geofront and maintain your position there."

Naomi nodded and left the room. Producing a cigar from his pocket, Big Boss placed it in his mouth and lit it. After taking a puff and blowing out the smoke, he said, "Naomi is like a daughter to me, but the last thing I need is for her to tell me how smoking is bad for my health."

Despite the situation, Ritsuko felt a little more at ease. "She told me the same thing," she said.

Big Boss slid the pack of cigarettes over to her, the lighter following close behind. After pulling out a cancer stick, lighting it, and taking a drag, Ritsuko calmed down...somewhat.

"At the moment, we are currently at the Japanese Strategic Self-Defense Force base about fifteen miles from Tokyo-3," Big Boss explained. "What Naomi has told you is the truth. Seele and Section 2 have orders to kill you. I simply brought you here to ensure your cooperation."

"By having Naomi disguised as me and sneaking into Terminal Dogma?" Ritsuko asked.

"War is based on deception," Big Boss explained. "Always has been, Doctor. Having a death sentence on your head makes a good motivator, wouldn't you agree? No one knows you're here, and if you wish to stay alive, then you should cooperate with me."

"If I say no?"

"You will be placed under arrest and handed over to the U.N. for crimes against humanity, as an accomplice in Gendou Ikari's schemes for Third Impact. I think that screwing the man who caused Second Impact would not look very good for you in the long run."

"Gendou caused Second Impact?" Ritsuko said. "What proof you have of this?"

"He was present, along with Zero at Mount Markham, where ADAM was discovered," Big Boss explained. "He sabotaged Doctor Katsuragi's 'contact experiment' with ADAM's core, on Zero's orders. Then he left for Japan, knowing full well what was going to happen the following day." His face was a grim line. "Your boss just so happens to be the biggest mass murderer of all time. He's so evil that even the Devil himself would not trust him."

"What about Seele? How do you know about them?"

"Easy," Big Boss replied, remembering Zero's confession. "I know the head boss. His name is not Keel Lorenz, not is he even a German. His real name is David Oh, a British national, and my former commanding officer fifty years earlier. I knew him as Major Zero. Zero and I have a personal score to settle."

"But..." Big Boss continued, "cooperate with me and tell me what I want to know, and I have the guarantee of the Prime Minister and the Secretary General that you will be given general amnesty and immunity from prosecution, in exchange for your testimony. They will be offering Deputy Commander Fuyutsuki the same deal."

"How do you know the Secretary General and the Prime Minister?" Ritsuko asked, curious as to who Big Boss' connections are.

"Old war buddies from FOXHOUND," Big Boss explained. "The only two members that Seele could not buy off." He paused for a moment to take a drag from his cigar. "Your mother designed the MAGI supercomputer, who was also head of Project E following the death of Yui Ikari. Quite a famous woman, your mother. Because of your relationship with Gendou, you know what he has planned, yet you share his bed. He is manipulating you, Doctor, as he did your mother."

Ritsuko puffed at that. "You know nothing. He loves me. I know it."

Big Boss shook his head. "No. Gendou's just using you, the same way he used your mother. He is a master manipulator, but he is nowhere near the level of Zero. Zero saw the potential Gendou had and took him as his student. However, given the recent failures that Nerv has suffered, as well as Gendou's personal stake in this, Zero no longer trusts him."

Ritsuko wasn't convinced. "Just what does someone like you know about love?" she spat as she reached for another cigarette.

To answer Ritsuko's question, Big Boss reached into his front pocket, pulled out a photo, and handed it to Ritsuko. The photo itself was five decades old, but to Big Boss, it brought him luck.

The picture was that of EVA, dressed in the same outfit she wore following Operation Snake Eater; the khaki coverall, zipped down, exposing her bikini top, the gun belt around her waist, containing her Chinese-grade Mauser, and her combat boots.

Snake had taken the picture of her, several months after rescuing her in Hanoi. She was standing beside a motorcycle, smiling for the camera.

Ritsuko flipped the picture over. It had a lipstick stain on it, as if she had kissed the photo. Aside from that, was a small message, which read:

**For luck, Jack. Love, E.**

"I maybe a soldier," Big Boss said, retrieving the picture and placing it back in his pocket, "but I know some things about being loved. We were together for over fifty years, before Seele killed her and my old comrade in arms back in Prague. Part of my mission is motivated by vengeance, as well as preserving Humanity from Seele and Gendou's intentions. As far as I'm concerned, both Zero and Gendou will not live to see The Hague. You will not live to see another day unless you simply open your eyes to the truth."

"I read the reports myself," Ritsuko said. "My mother died from blunt force trauma after crashing her car. The reports are legit."

Big Boss shook his head. "You've been fooled, Doctor. Forgive me, but you must know the truth." Turning to the door, he called for FOXHOUND's resident computer hackers and geniuses.

Otacon and Mei Ling entered the interrogation room, the latter holding a laptop.

"This is Ritsuko Akagi, chairwoman of Project E for the anti-angel Agency Nerv," Big Boss conducted the introductions. "Dr. Akagi, this is Dr. Emmerich and Miss Ling, computer specialists for FOXHOUND. With the help of hackers from the JSSDF, they managed to gain access into the MAGI, and found several pieces of evidence that will most likely change your mind."

"What?" Ritsuko gasped. "How in the hell did you hack into the MAGI? The system is foolproof!"

"Trade secret," Otacon replied, as Mei Ling set up the laptop.

After punching in several keys, Mei Ling spun the laptop around. "This is the video from the Gehirn facility, now known as Nerv Headquarters, dated 4 November 2010. The date in which your mother, Dr. Naoko Akagi, supposedly had died in her fatal car accident."

Ritsuko watched the surveillance video with growing horror.

[Another clip out of Evangelion. We are at the bridge, where Naoko Akagi is hard at work. Behind her, a four-year-old Rei Ayanami enters the bridge, startling Naoko.]

NAOKO: Who's that? Who's there? (Sees Rei) Oh, it's you, Rei. Is there something I can help you with?

YOUNG REI: No. I got lost.

NAOKO: Maybe I should help you to find your way then?

YOUNG REI: No, I will find the way on my own.

NAOKO: And how, pray tell, will you do that?

YOUNG REI: Why should I tell you, you old hag?

[Naoko is taken aback at this insult from this little girl.]

NAOKO: It's not nice to call someone an old hag.

YOUNG REI: But aren't you an old hag?

[Now Naoko is starting to get angry.]

NAOKO: That's enough out of you, young lady! Wait till Commander Ikari hears about your lack of manners!

YOUNG REI: Why? He calls you that all the time.

[This catches Naoko off guard. She wasn't expecting this, not from the guy who she was sleeping with. Rei continues to twist the knife, unknowingly.]

YOUNG REI: He's always saying 'The old hag goes on my nerves. I don't need the old hag any longer.'

[Now Naoko is VERY PISSED off. Before Rei could say or do anything else, she is out her seat, her hands around Rei's neck, strangling the girl.]

NAOKO: You...you little bitch! You're just like me...replaceable!

[This goes on for a full minute, Rei pounding on Naoko's arms, her attempts growing weaker and weaker, until Naoko comes to her senses. But it's already too late. Naoko releases her grip on Rei, who falls to the floor, lifeless. She backs away from her victim, horrified.]

NAOKO: (whispers) Dear God. What have I done? (screams) WHAT HAVE I DONE?

[Naoko throws herself from the top part of the bridge. Her head impacts the MAGI's housing with a sickening CRACK, bouncing off said casing, before falling to the bottom floor. Her body twitches for several minutes, before lying still. Fast-forward to about 20 minutes later. Security forces are at the scene of the crime. The body of Rei Ayanami has been carted away. A younger Gendou Ikari and Kouzou Fuyutsuki are standing over the covered body of Naoko Akagi.]

GENDOU: Professor...go to Terminal Dogma and wake up Rei II. I will clean things up here.

[Fuyutsuki nods and leaves the scene. Gendou retrieves a cellphone from his pocket, and dials a number.]

GENDOU: Hello, Ritsuko? This is Commander Gendou Ikari of Gehirn. I am sorry to report to you that there has been a dreadful accident regarding your mother. She lost control of her car and crashed. I'm sorry, but she did not make it. There was too much trauma to the head. She did not suffer. Yes, I will release the body so it can be given a proper burial. You're in Tokyo-2? Then come back to Tokyo-3 and claim your mother's body.

[Gendou ends the call and dials another number.]

GENDOU: This is Commander Gendou Ikari, Level SS clearance. I need a report on a car accident regarding Naoko Akagi made. Also, take her car and destroy it. And send someone to the bridge to clean this mess up, as well as a technician to replace the housing on the MAGI. Ikari out.

[Gendou ends the call. He pockets the cellphone and looks down at the body of Naoko Akagi.]

GENDOU: It has been fun, Naoko, but your usefulness has run its course. I'm sure that your daughter will be more satisfying in bed that you will ever be...you old hag.

[Gendou walks away. The video ends here.]

As soon as the video ended, Ritsuko felt sick to her stomach. Literally. In fact, she made a beeline to the nearby trash can, and promptly emptied the contents of her stomach inside the trash can.

As she continued to vomit, Otacon and Mei Ling departed from the interrogation room. Only Big Boss remained behind.

Ritsuko's mind was racing. Gendou had been stringing her on ever since her mother's death.

'That is what it ultimately boils down to...control.'

Naomi's words came back to her in full force. Apparently, control over Shinji wasn't enough. Gendou used her as well. He used her mother, his son, damn near everyone in Nerv for his own desires.

"I'm sorry that it has to be this way, Doctor," Big Boss said, sympathetic, yet professional, crouching over Ritsuko, his guard not completely down. "But you had to see for yourself the truth about Gendou. He never cared for you, nor your mother. But can help make things right. Help us stop Gendou from unleashing Third Impact."

Ritsuko coughed the last of her breakfast and coffee into the trash bin. Turning her head so that she could look at the older man, she gave her answer.

"I'll do it. I'll take the deal. Can you protect me from Gendou and Seele?"

Big Boss nodded. "No one, with the exception of my senior members, as well as the Secretary General and the Prime Minister, know that you are here. At the moment, Seele and Section 2 are following false leads that I've had leaked out. It will keep them going in circles for the moment."

At that moment, there was a knock at the door, followed by Ocelot's voice. "Boss. There's an Angel hovering over the Matsushiro ruins. I've notified the others. We're on our way to the computer room."

"I'll meet you there," Big Boss said. Turning to Ritsuko, he said, "For your own safety and protection, you'll remain here for the time being."

Ritsuko nodded, and Big Boss took his leave, the door locking behind him. Ritsuko sat on the floor, her back against the wall, hugging her knees as she slowly came to terms about her mother's relationship with Gendou Ikari.

* * *

Nerv Headquarters, The Geofront

The Angel that was currently hovering over the Matsushiro ruins had the appearance of a double-helix.

Armisael, the Angel of the Womb, has come.

It had appeared over the Matsushiro ruins, and soon, would make its way to Tokyo-3 within the hour.

Misato Katsuragi entered the bridge, followed by Naomi Hunter, having returned from the JSSDF Base Haruna. "Status report," the major ordered.

"Reports coming in from the salvage crew at Matsushiro," Hyuuga reported. "It just appeared about 20 minutes ago. Pattern's shifting from blue to orange. I can't get a lock on it."

"Tricky little bastard," Misato muttered.

"Remove Unit One from cryo-stasis and prepare to transport both Unit Zero and Unit One to Matsushiro," Gendou ordered from his desk on the bridge, Fuyutsuki standing beside and behind him. "Classify as the Sixteenth Angel, and prepare to sortie. As of this moment, Pilot Ikari is back on active duty."

At that moment, a volley of rockets appeared on the screen, and detonated around the Angel, just as the pattern had changed back to blue.

"The hell? Who's firing on the Angel?" Misato shouted.

"No reports of JSSDF, or UN forces in that area," Maya replied. She then gasped. "It's that same mecha!"

Sure enough, the massive, Evangelion-sized mecha appeared on screen. Unlike RAYs 1 and 3 which were powered by a mini-fusion reactor, RAY 2 had a working Super Solenoid core, thus allowing it to project an AT-field like the EVAs. The Patriots, having pilfered a working S² Core from a secret Seele facility used to produce the cores for the mass-produced EVAs, right before destroying the facility took it back to Shadow Moses, and installed it inside RAY 2. Having learned from the mistakes of the Nerv facility in Nevada, in which the entire facility had been sucked into a Dirac Sea when they failed to take the proper precautions, The Patriots had successfully installed the core and brought RAY 2 online.

The rockets, however, had the desired effect of provoking the Angel. It had shifted from its double-helix form into a long, thick strand. Breaking apart, the long, wormlike strand found the offending target and retaliated.

RAY 2 raised its AT-field, but the Angel penetrated through it like a hot knife through butter, causing nasty-looking veins to appear, the sign of Angel contamination.

* * *

At the JSSDF Base Haruna...

"We have contact with the Angel," one of the techs reported as Armisael began to merge with RAY 2.

Big Boss watched the battle, along with Ocelot, and the rest of FOXHOUND on several monitors. Big Boss was well versed in how the EVAs worked, thanks to the JSSDF's hacking of the MAGI, as well as its AT-field capabilities.

Meryl watched the scene in shock. "I swear, I've seen weird stuff before, but nothing like this," she said.

Big Boss chuckled. "You should have been here when the war started months ago. I had a front row seat to the entire thing." He gestured to RAY 2. "One of the facilities we hit were producing the S² cores for the mass-produced Evangelions Seele intended to use to jump-start Third Impact. RAY 2 is designed for this specific purpose: to destroy the final Angel." To the techs, he said, "Invert the AT-field, and push it to maximum."

* * *

Back in Nerv Headquarters...

"An AT-field!" Misato gasped. "But...how...?"

"It appears that the mecha has a working S² core," Fuyutsuki said as he watched the Angel get absorbed into RAY 2.

"Yes...where are the pilots?" Gendou demanded.

"Inside the Entry Plugs," Fuyutsuki said. "We outfitted Rei's Unit Two with a special battery pack that will allow her an extra fifteen minutes of internal power."

"Good. I want that mecha."

* * *

JSSDF Base Haruna.

The tech turned to Big Boss. "General, the Angel has been absorbed into RAY 2, and the AT-field is holding."

Big Boss nodded. "Initiate the D-drive on RAY 2. Set it to maximum."

The tech nodded and punched in several keys. "D-drive initiated. Core explosion in T-minus sixty seconds."

"Boss, Matsushiro is close to Tokyo-2," Snake objected. "If you detonate the RAY, you can possibly destroy the city!"

"Tokyo-2 is at least 60 miles away from the testing facility," Big Boss replied. "The core explosion, say it took place in Tokyo-3. At least 70-80 percent of the city will be destroyed, so the blast will be contained. Plus, the mountains surrounding the area will absorb most of the explosion. The Secretary General and the Prime Minister have already been notified."

"I hope you're right," Meryl said. "Seriously. I hope to God you're right."

* * *

Nerv Headquarters.

Hyuuga had picked up the readings from his console moments later. Turning to Misato, he yelled, "Major! I'm getting readings from the mecha's core! It's going into critical mode!"

"Self-destruct imminent!" Maya shouted, "Core explosion in T-minus ten seconds!"

Misato saw that it would be pointless in launching the EVAs. "EVA Units Zero and One, stand down."

Gendou was about to belay that order when he felt a hand on his shoulder.

"It's pointless now," Fuyutsuki said, as Aoba counted down. "The mecha will be long since destroyed by the time Ikari and Ayanami will arrive. Let the order stand."

"…seven…six…five…four…"

Gendou growled. His scenario had called for Rei to die at the hands of Armisael. But with the destruction of the Dummy System and the Reiquarium, as well as Ritsuko's apparent defection and Asuka vanishing, his scenario was all but shot to hell. "Fine. Major Katsuragi's order will stand."

"...three, two, one," Aoba finished counting down.

* * *

Ruins of Nerv Matsushiro Facility.

RAY three spasmed as its core reached critical mass. The Angel, sensing its apparent doom, tried to escape.

But it was too late.

With the force of an N² mine, RAY 2 detonated, taking the remains of Nerv's Matsushiro facility with it, as well as destroying the Angel within its body. The force of the explosion had triggered several earthquakes in the region, which were felt as far as Tokyo-2 and Tokyo-3. Even the JSSDF Base Haruna in which Big Boss was hanging around in felt the tremors.

Nerv Headquarters.

The blast caused havoc on the sensors, as well as on the MAGI. It would be at least two minutes before the blinding light would clear.

"Report!" Gendou barked.

"Shockwave's knocked out all the sensors!" Maya shouted. "Wait a minute. Sensors are coming back online." She looked at her monitor. "The Angel is gone, sir. The mecha as well."

Gendou unsteepled his hands and leaned back in his chair. "Only one more Angel left. Then...then I can be with Yui once again," he murmured, looking at the screen. The entire Matsushiro facility was reduced to a giant, smoking crater.

Fuyutsuki wondered whether or not to tell Gendou that the war was over, that the Angel of Free Will had already been destroyed. In the end, he decided that Big Boss and the Patriots were much more scarier than Gendou and Seele, and decided to keep his mouth shut.

Misato got on the horn with the pilots of the two remaining EVAs. "Shinji...Rei...the Angel has been destroyed."

"Well that was easy," came the reply from the Third Child.

"I agree," said the First Child. "Returning to the EVA Cages."

* * *

JSSDF Base Haruna.

Big Boss entered the interrogation room. Ritsuko had not moved from her spot on the floor. Taking a seat in his chair, Big Boss gave Ritsuko the news. "Thought you would like to know that the war is as of this moment, over. The Angels are no more."

Ritsuko chuckled bitterly. "There's still one more Angel left."

"You mean Tabris, the Angel of Free Will?" Big Boss inquired.

Ritsuko's head snapped up. "What? How did you...?"

"I also have a copy of the War Scrolls in my possession," Big Boss explained. "Not to mention Mr. Kaji is my inside man, who let me know of Seele's intentions. Gendou can still use Unit One and the Lance of Longinus to unleash Third Impact, as well as the forbidden union of ADAM and Lilith. Kaji notified me that he delivered ADAM to Ikari. Where is it?"

"It's...it's grafted onto his right hand," Ritsuko replied. "I performed the procedure myself."

"Damn. Should have shot the other hand," Big Boss muttered.

"You said that there were no more Angels. How did you know about Tabris?" Ritsuko asked.

"Simple. Kaji's clearance as a Seele operative has worked out in my favor. He was to be chosen by the Marduk Institute as the Fifth Child, following Ayanami, Sohryuu, Ikari, and Suzuhara respectively as a replacement pilot for Sohryuu, under the name Kaworu Nagisa."

Ritsuko recognized the name. As Big Boss had mentioned, he was the designated Fifth Child. But he did not show.

"Tabris is dead," Big Boss said. "And a major factor in Seele's plans has been removed." Off Ritsuko's confused expression, Big Boss continued. "Over the world, Seele has been manufacturing parts for twelve mass-produced Evangelion units. The parts were then shipped to Hokkaido, to a hidden facility in Mount Tarumae, where the EVAs were constructed."

Big Boss paused for a moment to allow Ritsuko to make the mental connections. "Seele used the Tarumae facility to build the EVAs. And that mecha that was seen in the city...?"

"The next-generation Metal Gear RAYs," Big Boss said. "Each one outfitted with anti-EVA technology, as you have witnessed in the battle with the Fifteenth Angel. I used the RAYs to attack the facility, and destroyed the EVAs, as well as Tabris. The N² mine was overkill, but it did the job. By removing Seele's trump card in their scheme for Instrumentality, they have no other choice in having to invade the Geofront in order to wrest control of Third Impact from Gendou. Seele knows about the attack on the Tarumae facility, and I'm willing to bet that they would make their move very soon."

He rose from his seat. "I'll have you taken to your temporary quarters. You will be under guard, or course, so don't try to escape. The soldiers have orders to shoot on sight."

* * *

On the surface...

Shinji had hitched a ride back to his apartment with Misato. Upon arriving at his housing complex, he was greeted with a very unwelcome sight.

Fire engines and the local police department had blocked off access to the apartment, which at the moment, half of the building was in flames.

Unfortunately for Shinji, his apartment was one of the buildings that had caught fire as well, leaving him virtually homeless.

On the bright side, Shinji still had his SDAT player, which was in his backpack.

The tremors that had resulted from RAY 2's explosion in Matsushiro had ruptured a series of gas lines in Shinji's part of town, resulting in four buildings being destroyed by the ensuing blasts. Fortunately, no one was killed in the explosions, since they were in the shelters during Armisael's attack, despite the Angel being miles away.

Shinji watched as the fire engines continued to work putting out the flames.

"Shinji."

The pilot of EVA Unit One turned around. Misato was standing by her car.

"Come on. Let's go home."

* * *

Katsuragi Asylum for the Drunk and (formerly) Aggressive, later on...

One month earlier, Shinji had moved out of Misato's apartment. Now, as he stood in the empty bedroom which was once his own, the events had come back full circle.

He was once again back in the place he considered to be home.

Misato, after downing three beers, had dozed off. Pen-Pen was happy to see him back, which meant that there would be no more of Misato's weapons-grade curry for him to eat.

A small box was in the corner. Upon inspecting it, Shinji saw that it was a box filled with some of his old clothes. Clothes he had forgotten to take with him following his rushed departure from this place back when Asuka lived here. The clothes were not tampered with, thankfully, allowing Shinji to change into a pair of shorts and a T-shirt after his bath.

The room was bare, Section 2 having removed Asuka's belongings from the apartment on Misato's orders.

However, there were two things that Section 2 had overlooked.

The first, a pair of crimson A-10 neural connectors, obviously belonging to Asuka. The second was a group photo taken shortly before Bardiel's attack at the Matsushiro facility, consisting of himself, Asuka, Rei, Misato and Kaji (done up in the MGS style of artwork), Asuka glomping on Kaji's arm, while Misato and Rei stood on either side of him.

Shinji picked up the photo and the connectors and exited the room. Walking out onto the balcony, Shinji hurled the three items out into the darkness. They landed neatly inside a waste bin, the photo having been sheared in two by a sharp piece of glass, severing Asuka's image from the other four images.

Walking back into his room, Shinji retrieved his SDAT and prepared to play Track 26 when his cellphone rang. Upon looking at the caller ID, he saw that it was Big Boss.

Shinji quickly answered the phone. "Boss?"

"How you doing, kid?" Big Boss' voice replied on the other end.

"I'm doing okay," Shinji replied. "How's things on your end?"

Earlier in the week, Big Boss had left for JSSDF Base Haruna. His explanation to Shinji was that he was training some fresh recruits to the JSSDF and would not be back for two weeks.

"Oh, you know how these training sessions are," the old man replied. "It's like a holiday. Good food, good wine, with lots of dancing girls, and parties."

Shinji laughed at that.

* * *

JSSDF Base Haruna.

Outside, Big Boss is on his PDA, watching Snake and Meryl practice their CQC. things had calmed down somewhat following the impromptu celebration signaling the conclusion of the Angel Wars. Now, only Seele and Gendou were left.

"I heard what had happened with Sohryuu," Big Boss continued.

"I'm not," Shinji replied. "You taught me that you fight only to survive. Sohryuu is the other extreme. She was more than willing to screw mankind over for personal glory. Then she had the Nerve to blame her screw-ups on me. Such a hypocrite."

"Shinji...I'm going to tell you something that I've told my son and my former pupil," Big Boss said. "We're not tools of the government, or anyone else for that matter. For me, I've always been good at fighting. But the difference is that I always fight for what I believe in. That's the difference between yourself and Sohryuu. You don't pilot not to satisfy your ego, or even to hear praise from your father. You pilot to defend all of humanity. For that, you have earned my respect."

He looked at his watch. "It's getting late, young Ikari. Time to call it a night. You have school in the morning."

"I know, I know," Shinji replied. "I'll see you when you come back. Take care of yourself, Boss."

"You too, Shinji," Big Boss replied as he ended the call.

* * *

The following morning, Big Boss, along with Ocelot, Ritsuko Akagi, and the two senior commanders of FOXHOUND, held a private conference with the Secretary General of the United Nations and the Prime Minister of Japan.

It was a video conference, held on a secure line. Should Seele try and listen in, Big Boss had taken precautions. The signal was garbled, mixed in with that of a local radio station in Tokyo-2.

The Patriots and their guest were inside the conference room on base. In front of them, were three monitors. The monitor on the left had the U.N. Secretary General. The one on the right was that of the Japanese Prime Minister. The last monitor was blank.

"Gentlemen, I thank you for answering my call on such short notice," Big Boss said. "As of yesterday evening, 1800 hours local time, the Sixteenth Angel, codenamed Armisael, has been successfully destroyed. The Angel Wars is now over. However, there is still the matter of both Seele and Nerv Supreme Commander Gendou Ikari. With the destruction of Armisael, Seele will more than likely use the Haven Shock Troops to invade the Geofront, should they fail to get the JSSDF to launch the assault."

"Big Boss, do you have a timetable?" the Secretary General asked. "When will Seele launch their attack?"

"We don't know," Big Boss replied. "But we do know where the Haven Troops are currently stationed, should Seele needs them to attack. And it appears that Seele is not taking any chances, since they are going to bring the full brunt of their forces upon the Geofront and Tokyo-3; five combat combat units, easily outnumbering the JSSDF's three."

A nod to Otacon and Mei Ling, both behind their laptops, and a picture came up on the third monitor. A satellite photo of the Korean Peninsula. In the violent turmoil following Second Impact, the Communist North had declared war on the Democratic South. The ensuing war between the two Koreas had ended in a victory for South Korea, thanks to the untimely demise of the Communist leadership, thus throwing the country into chaos.

Most of the northern part of Korea lay deserted. Perfect for Seele for an operations base for their Haven Troopers.

"This was taken three hours ago," Big Boss explained. "Seele is preparing for their final assault in order to wrest control of Third Impact from Gendou Ikari. This next photo is very disturbing."

Disturbing indeed, as it showed the black-and-red EVA, practicing with what appears to be a heavy lance. The next photo was that of the lance shifting into an even more deadly weapon; the Lance of Longinus.

"Is that an EVA?" the Prime Minister asked.

"Yes, Mr. Minister," Ritsuko replied. "Evangelion Unit Five, an advanced prototype of the production model EVA. This one has been outfitted with not only a fully functional S² core, but it is also armed with a replica of the Lance of Longinus, a weapon powerful enough to penetrate even the strongest AT-field."

"Who is the pilot of Unit Five?" the Secretary General demanded.

Next to the satellite photos, a dossier of Asuka appeared.

"Asuka Langley Sohryuu, former pilot of Unit Two," Ritsuko explained. "Father's American, named Daniel Langley, mother's 1/4 German and 1/4 Japanese, former Gerhin researcher Kyouko Zeppelin Sohryuu. Child prodigy with a 172 IQ. Was stripped of her duties as an EVA pilot and disavowed following several incidents, which led to her attacking the First Child, Pilot Rei Ayanami and the Third Child, Pilot Shinji Ikari. Diagnosed as a sociopath with an inferiority complex. She was to be sent back to Germany following her dismissal, but it is now apparent that Keel had her brought to him to pilot the EVA, in order to back the Haven Troops' invasion of the Geofront, not to mention that she has a score to settle with Pilot Ikari."

"Does Commander Ikari know about the fate of Tabris?" the Prime Minister asked.

"No. He's still expecting the final Angel to appear," Big Boss replied. "Which is why I propose we execute 'Susanoo's Wrath.'"

"Go on," the Secretary General said.

Big Boss laid out his plan. "My plan is this. We can't order a full-scale evacuation, because Seele will catch wind of it, and move their timetable up, so we'll use the air raid alarm to send the people into the shelters once we know that the FROGS are on their way. As long as the people are out of the way, then the FROGS won't hurt them. Then we move the JSSDF into position inside the Geofront, and fortify the defenses, while evacuating all non-military personnel. The U.N. crack troops can defend the city and the shelters from the Haven Troopers. There are may ways one can enter the Geofront, so that means we can't police them all. We will make our stand with the EVAs and Metal Gear RAYs. While the battle is going on, I will blow the lid off of Second Impact and expose Seele and Gendou Ikari."

"And Doctor Akagi?" the Prime Minister asked.

"For the past couple of hours, she has been forthcoming with vital information in regards to Nerv, the Evangelions, and the Geofront in general," Big Boss explained. "In exchange for the immunity deal we have offered her, she has agreed to help us."

"Is that true, Doctor?" the Prime Minister asked

Ritsuko nodded. "Yes. Certain evidence regarding my mother, Doctor Naoko Akagi has been brought to life by General Hayter," she said. "It is apparent that Gendou Ikari had drove my mother to suicide, not to mention that he has been using me as well."

"Consider yourself lucky, Doctor Akagi," the Secretary General said, "that you decided to defect to Big Boss' side." Turning to Big Boss, he said, "Boss, I trust you with my life."

"As do I," the Prime Minister said.

"You have the full backing of the United Nations armed forces," the Secretary General said. "You may commence 'Susanoo's Wrath' when the time comes. Good luck, and Godspeed."

"Good luck, Boss," the Prime Minister said.

"The both of you have my thanks," Big Boss said.

With that, the conference was over.

* * *

Following the meeting, Big Boss met with his inner circle, which consisted of the three JSSDF generals, FOXHOUND, and Ocelot.

Big Boss made his announcement. "I have received word that the JSSDF forward base near Futagoyama has been complete. Send the word to the rest of the troops. We will move there, since it's closer to Tokyo-3. In the meantime, we have to set up a ruse for Zero and Seele to think that this base is occupied." He turned to Otacon an Mei Ling. "Can you two send out fake communiques that Seele can pick up? Make it look like that there's a build-up of troops arriving at Haruna."

Mei Ling nodded. "Consider it done, General."

"So how are we going to pull this off, Boss?" Ocelot asked.

"Easy. We move in the dead of night," Big Boss explained. "The forward base is disguised as a civilian airport, so Seele nor Gendou will bat an eye." He looked at his watch. "We will begin tonight at 2345 hours. From here on out, we are at Stage Two battle alert. Dismissed."


	9. Episode 8: Battle For Humanity, Part 1

_**Episode 8: The Battle For Humanity! Seele vs The Patriots, Part One**_

Snafu's Notes: Here it is. The moment of truth. The battle between Seele and The Patriots, and more importantly, the final battle between Shinji and Asuka. Also, _**bold italics **_denotes speaking German. Also, for those who had PM'ed me about Zero's real name, his real name** is **in fact, David Oh. Seriously. Also, as you have seen in the chapter's title, this chapter is in two parts, since it was just as long as Episode 5. I had planned originally to post the chapter in its entirety, but I decided to rewrite several key portions in the second half of the chapter, as they were not up to my liking.

Upon discovering the location of the Haven Troopers' main base of operations, Big Boss had ordered around-the-clock survailliance on the base. Using several unmanned UAV drones outfitted with the stealth camo, The Patriots and the JSSDF forces went on high alert, ready for the moment where the order to execute 'Susanoo's Wrath.'

Named after the Japanese kami of storms and the sea, 'Susanoo's Wrath,' officially known as 'Special Order A-801,' is what Big Boss has explained to Gendou during his visit to the Geofront. Should either the United Nations or the Japanese government lose confidence in Nerv's abilities to keep humanity safe - or whether or not Gendou pisses off the wrong people, whichever comes first - then the Japanese Strategic Self-Defense Force, assisted with a battalion of United Nations crack troops, would occupy the Geofront and place Gendou Ikari under arrest.

Ritsuko Akagi had approached Big Boss and had voiced her opinions about Seele trying to hack into the MAGI. If Big Boss and the Patriots had successfully hacked into the supercomputer, then Seele could do the same thing.

It was Otacon and Mei Ling that had made the save.

"Aside from having a backdoor into Nerv," Otacon had explained, "we also uploaded a triple-firewall system into the MAGI. Something that Mei Ling and I have created. Should anyone from Seele try and hack into the system in an attempt to take it over, they'll receive a nasty surprise."

"Which is...?" Ritsuko had asked.

"Should they reach the third firewall," Mei Ling had replied, "then their files will be instantly copied and deleted, the files themselves going into the MAGI. Also, at a moment's notice, we can send the files regarding Second Impact and Seele to every major news and media network in the world and blow this whole thing open at Big Boss's request."

It was also during this time that the JSSDF forces had covertly moved closer to Tokyo-3. Big Boss had suspected that once Seele discovered that the JSSDF could not be trusted in launching the assault on the Geofront, he would move to quickly remove the JSSDF out of the equation. So Big Boss had ordered the JSSDF to move to the fallback base, which was closer to the city.

* * *

December 29, 2015 - two weeks after the end of the Angel Wars.

The city of Tokyo-3 has just celebrated the Christmas holiday and were looking forward to the New Year. There had been no Angel attacks for the past two weeks, and the people enjoyed the brief peace it had brought.

But for the people of Tokyo-3, that peace was not going to last very long.

* * *

It was early in the morning when Otacon received the reports.

Seele had attempted to hack into the MAGI.

And as expected, the triple firewalls had served their purpose, thus setting Seele's plans back even further.

* * *

Location - unknown.

The seven remaining monoliths that made up the power cabal of Seele had convened in an emergency meeting following their failure to take the MAGI supercomputer.

"We were expecting Ikari to execute a Type-666 protection program on the MAGI," Seele 06 reported, "but this firewall has all but erased all of Seele's files, but not before copying and transporting them to the MAGI inside the Geofront. Not even our best hackers can breach it."

Seele 01 - Zero in his Keel persona - listened on in deep thought. 'Just what do you have up your sleeve, Jack?' he wondered, knowing full well who was behind all of this. Zero had expected Jack to back down following his warning. But given the recent build up of JSSDF forces in the Hakone region of Japan, he saw that Jack was looking for a fight.

"It appears that seizing control of the MAGI is no longer viable," Seele 07 added. "There is no way around this firewall."

Zero then spoke. "I had wished to solve this without any bloodshed, but that is no longer possible. We will use the JSSDF to invade the Geofront."

"Chairman, that's impossible," Seele 07 rebuked. "They refused to carry out the orders! Three times the orders came down, and they refused each time!"

"Very well," Zero said. "We will use the Haven Shock Troops to invade the city and the Geofront. The invasion will take place in three hours."

"What about the JSSDF?" Seele 03 asked. "They can still be used to defend the city against the Haven Troopers."

"That problem will soon be rectified," Zero replied grimly. Seconds later, a holographic image which had the words **EVA Unit Five - SOUND ONLY** came up. "_**Sohryuu.**_"

"_**Yes, Chairman Lorenz?**_"

"_**You will accompany the Haven Troops into Tokyo-3. Once the city is secured, then you will move into the Geofront.**_"

"_**Remember our deal, Lorenz. Do what you will with the others, but Shinji Ikari is mine.**_"

"_**Of course,**_" Zero said, and ended the call. "Give the Haven Shock Troops their orders. Leave no survivors inside the Geofront. Only Gendou Ikari is to be brought in alive. Send the bomber to the Haruna base."

* * *

JSSDF Forward Base Futagoyama - 0920 Hours, local time.

The young tech ordered to track down Big Boss found him inside the motor pool, where he was talking to Snake and Ocelot. "Big Boss, sir!" the tech panted, clearly out of breath.

"Catch your breath, son," Big Boss said. "What is it?"

The tech said nothing. Instead, he handed Big Boss a sheet of paper. The old man scanned it. It was short and to the point.

**JSSDF BASE HARUNA DESTROYED BY N² MINE. HAVEN TROOPERS ON THE MOVE. WILL REACH JAPANESE AIRSPACE IN 47 MINUTES.**

Big Boss digested the news with his usual stoicism. He had suspected that Seele would try and wipe out the JSSDF in one fell swoop, which is why he had the soldiers move to the forward base near Mount Futagoyama in secret, thus moving the force closer to Tokyo-3. One thing about Big Boss is that nine times out of ten, he knew what Zero was planning.

Turning to the tech, Big Boss dismissed him.

"What is it?" Meryl asked.

"It's showtime," Big Boss replied. "'Susanoo's Wrath' is a go."

* * *

Warning klaxons erupted throughout the base. Within minutes, every soldier stopped whatever they were doing and prepared for the upcoming battle. FOXHOUND was no different. Within minutes, the three combat units of the Japanese Strategic Self-Defense Force were on the grounds, each man and woman prepared for the battle ahead.

Big Boss stepped onto the podium, followed by Ritsuko Akagi, Revolver Ocelot, Solid Snake and Meryl Campbell. Big Boss was dressed for the occasion; his trademark SNAKE Camo, the Patriot in one hand. Ocelot was dressed in the same outfit he had on during the Manhattan Incident, while Snake and Meryl were dressed in their respective Sneaking Suits (MGS4 version).

"ATTENTION ON DECK!" one of the JSSDF soldiers shouted, bringing the forces (Ritsuko, Otacon, Mei Ling, and the four Beauties being the exception) to attention.

Big Boss stood before his soldiers, inspecting them. The official cover story was that the JSSDF was originally formed following a war between China and Vietnam over some islands. In truth, the JSSDF were in fact, Big Boss' private army, which was backed by the Japanese government. For the past decade, Big Boss had trained them for this very purpose: to fight for humanity.

Big Boss wasn't for speeches, so he was direct and to the point. "In less than forty minutes, you will have the privilege and the honor to take part in a battle that will decide the fate of mankind. In that time, Seele will dispatch its Haven Shock Troops into Tokyo-3 and the Geofront in order to unleash Third Impact. This...we cannot allow. I know that some of you have lost loved ones in Second Impact, and in the following wars that had engulfed the planet. I share your grief. Now is the time to take your revenge."

The troops erupted into cheers. Big Boss raised one hand, and the soldiers became silent.

"I will not lie to you," Big Boss continued. "Some of you will not make it out of this alive. What we do in this life will echo in eternity. If you want to piss the Haven Troopers off, then survive. You have your orders. If the FROGS want a fight, then we'll give it to them. Move out!"

Several supply trucks were parked nearby. The soldiers piled into them, while Big Boss, Snake, Meryl and Ocelot commandeered a Humvee, while Mei Ling, Otacon, and Ritsuko commandeered a second Humvee. The Beauty and Beasts Corps, each of them clad in their battlesuits, took the last truck. Actually, Only Laughing Octopus and Screaming Mantis were inside. Crying Wolf and Raging Raven were outside, Raven in the air and Wolf running on the ground.

Ocelot was behind the wheel, while Big Boss was riding shotgun. "I've notified the Secretary General and the Prime Minister. The U.N. is sending their crack troops to Tokyo-3 to assist us in the battle."

"How many?"

"Four combat units."

"Good," was all that Big Boss said before Ocelot lead the JSSDF forces out of the base. He retrieved the picture of EVA from his jacket pocket and regarded it for a moment.

'EVA...my love...protect me in this darkest hour,' he thought as he pocketed the photo.

* * *

Nerv Headquarters.

Ryouji Kaji had gotten the call while he was on his way to water his melons. The call came from Big Boss, and it was brief.

"Mr. Kaji...it's time. 'Susanoo's Wrath' is a go."

The call went dead after that. Kaji knew what that meant. Seele was on the way with their troops. The unshaven man took the moment to check his sidearm, a government-issue Beretta PX4 Storm, making sure that a round was jacked inside the chamber. Once he saw that he was ready, he got Naomi on the phone.

"Doctor Hunter speaking."

"Doc, it's Kaji. Big Boss is on his way, and he's bringing in the troops."

Naomi immediately understood what that meant. Big Boss was executing 'Susanoo's Wrath.' Which means that Seele has launched their assault. "How long do we have?"

"About thirty minutes before Big Boss arrives with the JSSDF," Kaji replied. "Less than that before the FROGS arrive."

"Understood," Naomi said as she cut the call.

Kaji pocketed the cellphone and after retrieving his body armor and a carbine from his office, rushed off to find Misato. Fortunately for Kaji, she was inside her office, going through what was the bane of her existence - paperwork.

Misato looked up. "Kaji? What is it?"

"Big Boss is on his way here with the JSSDF," Kaji replied. "Seele is on their way with the Haven Troops to invade the Geofront."

That was all that Misato needed. Opening her drawer, she retrieved her H&K P8. Making sure that a round was chambered, she followed Kaji out of the office, Kaji explaining everything on the way.

* * *

The citizens of Tokyo-3 were not greeted with the Angel alarms that were a frequent part of their lives, but rather, by an air-raid siren, followed by an announcement from the Emergency Broadcast System.

_"Attention. A state of emergency has been declared for the Hakone region of Japan. All non-military personnel please report to your designated shelters immediately. This is not a drill. I repeat, a state of emergency has been declared for the Hakone region of Japan. All non-military personnel please report to your designated shelters immediately."_

However, as Shinji Ikari was at the moment, in the shower, he did not hear the sirens, nor the announcement on the T.V.

* * *

The Geofront, Nerv Headquarters - Commander Ikari's office.

Gendou Rokubungi Ikari sat behind his desk as the reports were coming in.

The JSSDF were moving into Tokyo-3.

Gendou had long suspected that Seele would use the Japanese armed forces to invade Nerv. Only this time, as Gendou continued to read the report, the Japanese Strategic Self-Defense Force were not invading the city, but rather taking defensive positions in key locations around Tokyo-3, as the city went into fortress mode.

'Just what you are thinking, Keel,' the supreme commander thought. 'The last Angel has not appeared yet...this is not part of the scenario.'

He was still in the dark about the fate of Tabris and that of the nine mass-produced EVAs Seele had originally intended to use for their scheme of Instrumentality.

He was also in the dark about the fact that as of this moment, the JSSDF were at the moment, moving into Nerv Headquarters itself. That is, until he got the call from Fuyutsuki.

"Professor, what is going on?" Gendou demanded.

"The JSSDF is here," Fuyutsuki replied.

Gendou went rigid in his seat. "Where is the Major?"

"Major Katsuragi is with the senior commander. It's **him**."

Gendou's eyes widened.

General Hayter was here...again.

* * *

Central Dogma.

Kaji had filled Misato in on the details. Upon meeting with Big Boss in the corridors of Central Dogma, the old man himself had verified it.

The Tactical Operations Director was on the phone with Hyuuga as she led Kaji, Big Boss, Snake and Meryl down the hall, as JSSDF troops rushed by them, taking up their positions. Ritsuko had taken Otacon and Mei Ling to the bridge. "That is correct, Lieutenant. We have incoming. As of this moment, we are at Stage One Battle Alert. Send all non-combat personnel the shelters immediately. Shut down all monorails leading in and out of the Geofront. Lock down the entire base."

"But Major, we can't do anything about the Freight Entrances," Hyuuga objected. "They remain open 24/7!"

"It can't be helped," Misato replied grimly. "You have your orders, Lieutenant."

"Understood, Major. Hyuuga out."

Misato pocketed the cellphone.

"Where's Shinji?" Big Boss asked.

Misato froze in her steps. "Dear God...he's at my apartment."

"We're gonna need his help," Big Boss said. "Seele isn't taking any chances. They have an EVA in their possession - an advanced prototype. I'm sorry to say this, but it's been verified that Asuka Sohryuu is the pilot."

Misato looked at the old man. "Asuka is the pilot?" she asked, horrified.

Big Boss nodded. "Afraid so. She has joined forces with Seele in an attempt to get to Shinji. We need to get to Shinji before the FROGS do." He gestured to Snake and Meryl. "These two will accompany you. Now go, Colonel. We're almost out of time."

Misato nodded as she led Snake and Meryl down the hall. She then stopped and turned around. "Wait...Colonel?"

Big Boss turned around, the ends of his mouth twitched upwards in a small smile. "The U.N.'s issued a battlefield promotion for you, Lieutenant Colonel Katsuragi, for your efforts in the Angel Wars. That and Commander Ikari will soon be deposed for his crimes. Now go. Bring Shinji here."

Misato nodded. "Yes, sir." Turning to Snake and Meryl, she said, "Come with me."

As Misato led the two Patriot operatives down the corridor, warning klaxons began to blare, followed by an announcement by Maya Ibuki.

"Attention! All non-military employees please proceed to the nearest shelters immediately! We are at Stage One Battle Alert! I repeat, all employees proceed to the nearest shelters immediately!"

* * *

[The invasion of the Geofront takes place the same way as seen in End of Evangelion. Only this time, the FROGS are doing the invading on Seele's orders. Two of the Nerv guards are gutted, while a third is garroted from behind. Several bombs go off, killing several more Nerv guards, which is followed by the FROGS moving into the Geofront. Only this time, as the FROGS move into the base, they run into the JSSDF, who had taken defensive positions all over the base. The FROGS are armed with their standard PN-90s, while the JSSDF are armed to the teeth with assault rifles and heavy machine guns. The battle for the fate of humankind has begun.]

* * *

"The Daigatake tunnel has been cut off! Fire at the West No.5 freight entrance!"

"JSSDF forces have made contact with the invading force on Level 1!"

"The south hub station is off-line!"

"Contacts in Computer Room No. 77 and No. 3 hub-station!"

"Level 3 Block B report contact with Haven Troopers! Enemy contact in Block F! The main bypass is also under fire!"

As all hell broke loose all around the Geofront, Gendou Ikari arrived on the bridge, along with Deputy Commander Fuyutsuki and an armed escort of Section 2 guards. Upon arriving at the bridge, Gendou saw two people he did not recognize, a Chinese woman in JSSDF fatigues and a long-haired gaijin with glasses, also in JSSDF fatigues, both typing feverishly over their laptops.

The two armed men – the dark-skinned man and the Caucasian with the mohawk brought their guns to bear on Gendou, who froze in his steps.

He also noticed that standing alongside Naomi Hunter, was Ritsuko Akagi, and the last person he wanted to see.

Big Boss had noticed the soon-to-be deposed supreme commander's entrance. A snap of his fingers, and a squad of JSSDF shock troops appeared, assault rifles trained on Gendou and his entourage.

"What is the meaning of this?" Gendou demanded. "I am the supreme commander of Nerv! How dare you bring armed troops into my base!"

"Not anymore you are not. You've been relieved," Big Boss said. "As of this morning, the United Nations has issued Special Order A-801, codenamed 'Susanoo's Wrath,' which calls for the immediate abolishment of special legal protection of the anti-Angel agency known as Nerv and transfer of command to the Japanese government. As of this moment, you have been stripped of your duties of Supreme Commander of Nerv and is hereby placed under arrest. Deputy Commander Fuyutsuki is in command of Nerv as Acting Supreme Commander, with Colonel Katsuragi as Acting Deputy Commander."

"Under arrest? What for?"

Without breaking eye contact, Big Boss addressed not only Maya, but all present. "Crimes against humanity, as well as the crime of genocide in regard to the incident on 12 September 2000, also known as Second Impact, and conspiracy to commit mass murder and genocide in regards to Third Impact."

The entire bridge went silent at that very moment, the sounds of gunfire erupting from the various corridors of the headquarters was only heard. Gendou Ikari, the man who had led humanity through the Angel Wars was responsible for Second Impact?

Fuyutsuki then verified it. "General Hayter is telling the truth. I had also discovered the truth behind Second Impact shortly after the event had taken place. Ikari had threatened me with death if I had told anyone about it, as well as his schemes for a Third Impact."

The temperature in the room had dropped considerably. Even Gendou's Section 2 escort were giving him nasty looks. Sure most of Section 2 had consisted of hired muscle and thugs, but even they drew the line when it came to working for a man who made Hitler, Pol Pot and Stalin look like chumps when it came to genocide. After all, most of them had lost family members in the aftermath of Second Impact.

"You..." Gendou sputtered, his body shaking with rage as he glared at Fuyutsuki. "You...you dare betray me, Fuyutsuki?"

"It's over, Gendou," Fuyutsuki said. "Yui would have been horrified as to what you have done, as well as what you have become. There are no more Angels coming. Tabris has been eliminated a month earlier, on Big Boss' orders, and the mass-produced EVAs Seele planned on using for Third Impact have been destroyed. Why else would Seele be attacking us?"

Gendou's eyes narrowed at his traitorous professor. Then they widened. Big Boss? General Hayter is Big Boss, the legendary soldier thought to have died in Zanzibarland the year before Second Impact? But more importantly, there were no more Angels?

Before he could ponder this further, Big Boss broke his chain of thought, giving his order to Nerv's Section 2. "Escort Mr. Ikari to the holding cells and keep him there until this matter is over with," he said.

Two of the Section 2 agents grabbed Gendou by the arms and proceeded to escort him out of the bridge.

Fuyutsuki turned to Big Boss. "Well, General...I'm not a soldier. I will relinquish command to you."

"Glad you see things my way," Big Boss replied. He turned to Otacon and Mei Ling. "You two, get inside the MAGI. Send the reports regarding Second Impact and Seele to the world's news and media, as well as to the world's governments. Also, prepare to flood the corridors with bakelite on my command."

Otacon and Mei Ling nodded. As the pair went to work on the supercomputer, Big Boss turned to Fuyutsuki. "The biggest threat to Seele are the EVA pilots. Which is why the EVA Cages will be placed under heavy guard, the EVAs themselves ready to launch at a moment's notice."

Fuyutsuki nodded. He turned to the bridge bunnies. "You heard the General. Give the orders to the techs in the EVA Cage! Have them prep Units Zero and One!" He sighed.

Big Boss caught onto it. "Something on your mind, Professor?"

"It appears that man's ultimate enemy is not the Angels, but man himself," Fuyutsuki replied. "Of course, you already know as much, General."

"War. It never changes," Big Boss mused. "The Haven Shock Troops has five combat divisions to the JSSDF's three. But I got faith in my soldiers. We will see this through."

Meanwhile, Makoto and Shigeru had taken out their Nerv-issued P8 pistols.

"This is bad," Hyuuga said as he loaded the gun. "I don't think Nerv was meant to survive a human invasion."

Aoba nodded as he loaded his own pistol. "Yeah. This is only counter-terrorist measures at best."

"At least we got the JSSDF on our side," the bespectacled male bunny said. "Otherwise, we would not stand a chance." He looked at Maya. She was at her desk. Her gun was still in its case. "Maya?"

"I...I can't shoot," she admitted. She slammed her fist on the console. "Damn it! This isn't training! I wasn't shooting at people back then!"

Before Maya could break down, Ritsuko placed one hand on her pupil's shoulder. "Maya. Calm down. This area is well-defended. The Haven Troops will have a difficult time in reaching command. Just do your job and everything will be fine."

Maya calmed down. "Okay, Sempai. I'll do my best."

* * *

As Misato's Renault zoomed through the abandoned streets of Tokyo-3, they could hear the gunfire erupting from various parts of the city.

She prayed that she could make to Shinji in time as she made her car go faster, ignoring the screams of Snake and Meryl as she avoided another parked car by scant inches.

* * *

Katsuragi Asylum.

Shinji heard the gunfire as he got dressed. Looking out the window, he saw several cargo plans fly overhead, dropping paratroopers in the downtown area, which was followed by even more gunfire.

'What the...? We're being invaded!' Shinji thought. From the look of things, the invaders were human. One thing for certain, he had to get to the Geofront. And fast.

The house phone began to ring. Shinji was on it in an instant. "Hello?"

"Shinji! Thank God you're all right!"

"Misato?"

"I'm on the way to pick you up! I should be there in five minutes! There should be a Section 2 agent outside! Let her in, she'll keep an eye on you until I get there!"

Once the call ended, Shinji rushed to the door and opened it. Sure enough, the Section 2 agent was standing outside. Shinji recognized her from the school when Asuka had attacked him in a rage.

The woman entered the apartment. "I just got off the phone with Katsuragi," she said. "Just sit tight, and she'll be here soon."

Shinji nodded. "Okay."

* * *

The seven monoliths that made up Seele were monitoring the assault on Nerv Headquarters, which much to their surprise, turned out to be a full-blown battle between the JSSDF and U.N. crack troops versus the Haven Shock Troops.

This was supposed to be a simple assault. Instead, Seele found that their plans for Human Instrumentality could be derailed.

"This is unexpected!" Seele 07 said. "We were certain that the JSSDF were obliterated in the N² blast! Were not expecting them to fight the Haven Troops!"

"There are reports of fighting above Tokyo-3 and in the Geofront, with U.N. Special Forces backing the JSSDF!" Seele 03 shouted. "Our political maneuvering within the United Nations is all but gone! We can't call the U.N. Troops back!"

"Furthermore, I've been getting reports from all over the world!" Seele 11 shouted. "We've been exposed! The whole world knows the truth about Second Impact and our plans for Instrumentality!"

Seele 01 – Zero in his Keel persona – growled. There was only one person he knew was responsible for exposing his plans.

A certain, bearded, one-eyed soldier.

"Snake...**SNAKE!**" Zero screamed, thus dropping his Keel persona.

* * *

Meanwhile...

"Damn it! Unhand me!" Gendou shouted. "I am still the commander of Nerv! Unhand me at once!"

"Shut up," one of the Section 2 agents said, smacking Gendou in the back of the head. "You're no longer in control. Better yet, maybe we should just put a bullet in your head and tell Old Man Fuyutsuki that you tried to escape. No big loss. No one's gonna miss him. Hell, even his own son thinks he's scum."

"You're thinking about that too?" another Section 2 agent said. "This fucker deserves to die. I had family in South America when the Impact hit! We should at least torture him first, before killing him!"

As the former commander and his escort rounded a corner, they ran into three armed members of the Haven Shock Troops.

"What the fu...?" the first Section 2 agent said before the three FROGS turned on them.

"There he is!" the first FROG shouted, just as the trio opened fire with their PN-90s.

Gendou had the good sense to duck and retreat back around the corner, while his Section 2 escort was gunned down.

"Stop it!" the second FROG shouted. "Hold your fire! Keel wants him alive!"

Gendou heard that remark as he opened a secret passage and slipped inside. As the FROGS rounded the corner, Gendou was nowhere to be seen. "Where is he?" the FROG demanded as her two counterparts executed the surviving Section 2 members.

Gendou looked at his gloved hand, feeling the embryo grafted to his skin. 'So...Keel wants me alive because I have Adam,' he thought. 'Sorry, old man. You won't be able to stop me from reuniting with Yui.'

At least he still had his cellphone. Which means that he had one more lose end to tie up.

His son.

Gendou's decision was instant. His son no longer had a use for him, which means one thing to Gendou.

Despite the fact that he was his son, Shinji Ikari must die.

He retrieved it and placed a call to the female Section 2 agent that was at Katsuragi's apartment.

"Sir?"

"Is Pilot Ikari with you?"

"Yes, sir. I am watching him until Colonel Katsuragi arrives."

"You have new orders. Terminate the Third Child. Immediately."

"Sir?"

"I will not repeat myself, agent. You have your orders. Terminate Pilot Ikari now."

With that, Gendou ended the call, and prepared to take the long way back to his office. 'Yui will understand,' he thought. 'Everything I do, I do it for her.'

* * *

The Geofront.

While the FROGS stormed Nerv Headquarters, two of the combat units were outside in the middle of a deadly firefight with the JSSDF. The FROGS' acrobatic abilities easily matched the JSSDF's heavy firepower.

But the JSSDF had a trump card on their side.

From her sniping post, Crying Wolf – inside her battlesuit – aimed her rail cannon at the group of FROGS. After five seconds, her gun was at full charge.

"Now...let me hear you **CRY!**" Wolf snarled as she pulled the trigger.

**BOOM!**

Nearly half a dozen Haven troopers were sent flying from the deadly blast. Wolf fired off a second time, with the same results. Settling back into her battlesuit, she charged at the FROGS that were firing on her, their bullets bouncing off harmlessly against her armor.

Three of them were in the trees. Not a problem for Wolf, as she charged head-first into the tree, causing it to fall from the impact, crushing the FROGS under its weight.

Wolf the vanished into the forest once her rail gun was charged to full power. Then she fired again, and more Haven troopers were sent flying.

* * *

Nerv Headquarters – Central Dogma.

The Haven Shock Troopers had made their way inside Central Dogma, only to find a nasty surprise waiting for them. Instead of Nerv personnel, they found a welcoming committee of JSSDF and U.N. Forces within the halls of Central Dogma. Revolver Ocelot himself led the assault.

In rapid succession, he took out six Frogs with one Colt Single Action Army, before switching to a second Colt Revolver. The FROGS quickly took cover behind the wall, after seeing the wily gunslinger take down six of their comrades.

Not that it would stop Ocelot. Six more shots later, and the FROGS were down for the count, Ocelot had caused the bullets to ricochet, thus killing the assailants.

Ocelot's CODEC came to life as he reloaded his revolvers. "Ocelot, pull your men back. The FROGS are are bearing down on your position. We're going to seal off that corridor and flood it with bakelite," Big Boss ordered.

"Understood, Boss," Ocelot acknowledged. To the troops behind him, he gave the order to withdraw.

Seconds later, three squads of FROGS came charging down the corridor, expecting a firefight, only to find the halls littered with bodies of their fallen soldiers. The JSSDF had pulled their wounded back.

Then the blast doors in front of them sealed shut. It was then the lead FROG realized that it was a trap.

But it was too late.

The blast doors behind them slammed shut. Seconds later, the blood-red fluid that was bakelite flooded the corridor. The FROGS did not have a chance of escape as they drowned in the bakelite.

* * *

In another part of Central Dogma, a squad of FROGS found themselves face-to-face with the commander of the Beauty and Beasts Unit.

Clad in her battlesuit, with a Psycho Mantis doll in one of her 'hands,' and a Sorrow doll in the other, Screaming Mantis hovered over the FROGS, dodging their automatic fire.

Mantis laughed at their pitiful attempts to hit her with their weapons. "Let me hear you scream! Howl! Roar! From the very depths of your soul!" she snarled.

The Haven Shock Troopers were one of the very few PMCs that still used the nanomachines to make them even more combat effective. As it turned out, it would be their undoing. The lead FROG took cover as a volley of knives took down her fellow soldiers. Mantis' specialty – aside from being a medium – was that she could control anyone with nanomachines in their bodies. The Haven Shock Troopers were no exception.

Like a living wall of steel, the knives danced around Mantis' body. As the FROG stepped out from her cover, Mantis made her move.

The FROG froze in its tracks, as if something was possessing its body. As five more FROGS appeared, Mantis used the FROG she captured to gun down her comrades. Once they were dead, Mantis turned her attention to her captive. Lifting the FROG into the air, Mantis used her powers to snap the Haven Trooper's back in two, before discarding the body.

Several more FROGS appeared inside Central Dogma. This time, they were gunned down by their dead comrades, Mantis using their nanomachines to do her bidding. Once they were taken care of, Mantis retreated further into Central Dogma.

* * *

Three of the FROGS were sledgehammered back, dead before they hit the ground.

"Heeheehee," Laughing Octopus snickered as she brandished her own PN-90, throwing another FROG to the ground with her tentacles. "Isn't this funny? Laugh with me!"

Octopus opened fire on the FROGS, who returned fire, but to no avail, as Octopus retreated in a black cloud of smoke. However, the FROGS moved too soon, as they triggered several microbombs that Octopus had left in her wake, thus triggering another flood of bakelite, Octopus narrowly escaping as the blast doors closed behind her.

* * *

At the Katsuragi Asylum...

The female Section 2 agent got off the phone with Gendou Ikari. The whole city was about to go to hell, and he just ordered her to put a bullet into his son's head.

Oh, well. Orders are orders.

Shinji was in the kitchen, fixing himself a cup of tea in order to calm himself down as she pulled out her handgun. Screwing a silencer on the threaded barrel, she flipped the safety off, preparing to end the life of the Third Child.

'Sorry, kid,' she thought as she took aim to the back of the skull. It's nothing personal. Just business.'

However, Shinji Ikari would not die today.

"SQUAK!"

**POKE.**

"OW!"

It was Pen-Pen who had made the save. The hot springs penguin had just finished its bath and was on his way to the kitchen to grab a beer before heading for his fridge to relax and read about the mating rituals of hot spring penguins when he saw the strange woman pull her gun from her holster. Sensing Shinji's life in danger, Pen-Pen waddled over to the woman, who thankfully did not notice him, and poked hard at her leg with his beak.

Sure enough, it had the desired effect of distracting the would-be assassin.

Shinji turned around and was about to chastise Pen-Pen for harassing the agent when he saw the gun in the woman's hand. The woman saw that her element of surprise was gone, and quickly reacted.

Shinji ducked low, just as the Section 2 assassin fired, the shot missing Shinji, and putting a hole in Misato's fridge (as well as destroying a row of beer). Shinji's fist impacted the woman's chin in the form of a quick uppercut, throwing her off balance, the gun falling out of her hand. Then Shinji proceeded to grab her by the jacket, and just as Big Boss had taught him, performed a textbook-perfect hip throw...

...sending the woman through Misato's living room table with a loud **CRASH**, reducing the hardwood item to kindling, and knocking the female assassin out cold.

"Very impressive, Shinji."

Shinji recognized the voice. "Misato?"

Standing in the doorway, guns drawn, were indeed Misato, along with Solid Snake and Meryl. The trio had arrived just in time to see Shinji put the Section 2 assassin through the table. Outside, gunfire and explosions are heard throughout the city.

"Not bad, kid," Snake complimented.

"CQC," Meryl said. "You're a real Big Boss, aren't you?"

Shinji looked at the man. Almost immediately, he recognized him from the FOXHOUND group picture. He looked like a younger Big Boss, only without the eyepatch.

"No way..." Shinji whispered. "You look just like the old man."

"I know. I'm his son," Snake admitted. "Call me Snake. The redhead's Meryl. We gotta go, kid."

"What's going on?" Shinji demanded as Misato scooped Pen-Pen in her arms.

"We're being invaded," Misato replied, shoving the penguin in Shinji's arms. "Let's go!"

The three adults, plus one teenager and one penguin, rushed back to the parking lot, only to find that several FROGS were already there, with orders to terminate Shinji Ikari. Misato, Snake and Meryl quickly took them down in a hail of gunfire.

"Damn," Meryl cursed as she reloaded her Desert Eagle. "Those FROGS move pretty fast."

"It's because Ikari here is a primary target for Seele," Snake replied.

"Me?" Shinji said.

"The Geofront's already locked down," Misato said. "But there's the south freight entrance. It stays open 24-7."

"So we head there," Snake said.

"But given the fact that the FROGS and the JSSDF and UN crack troops are currently fighting in the streets," Misato pointed out, "we're gonna have to take the long way around. You think you and Major Campbell got enough ammo?"

"No need to worry about that, Major," Snake replied. Pointing to his bandanna, he said, "Infinite ammo."

"Oh."

In the firefight, Misato's car was an unfortunate casualty. The blue Alpine Renault would not start again. But there was the black Dodge Charger that Section 2 primarily uses.

A smile appeared on Misato's face as she walked over to the car. Snake and Meryl both exchanged worried glances before following her to the car. Shinji already had an idea as to what was going to happen next.

* * *

The streets of Tokyo-3.

[The following caption appears in English and Japanese: **Tokyo-3: City Streets.** Just as how the motorcycle chase in Groznyj Grad opens up in Snake Eater, so does the high-speed mad dash to the Geofront, from the rear of the car, the Charger turning a hard right to avoid the main streets, where the main skirmishes between the combined JSSDF/U.N. forces and the FROGS are taking place.]

Misato drove past a Haven roadblock, the four FROGS opening fire on the Charger as it zoomed past, pedal to the medal. Snake is riding shotgun, while Shinji, Meryl and Pen-Pen are in the back.

"Damn!" Misato cursed as she swerved around several abandoned vehicles, and another Haven checkpoint. "These bitches aren't making this easy for us!"

"Just get us to the Geofront!" Snake shouted. He then activated his CODEC. "Raven, do you read?"

In the skies above Tokyo-3, Raging Raven, flanked by a dozen of her drones, each armed with rockets, answered Snake's call. "Loud and clear, Snake."

"Raven. We need an escort to the Geofront. Track my CODEC signal."

Raven looked down, and saw the speeding Nerv sedan. "I got you, Colonel. Moving in."

Back inside the car...

"Misato, what the hell is going on?" Shinji asked. "Who is invading the city?"

"A power cabal called Seele," Misato explained as she kept her eyes on the road, which was at the moment, clear. But she still kept her manic driving. "They want to wrest control of Third Impact from your father, so they've ordered Haven Shock Troops to invade the city and the Geofront."

"The old fart has something to do with this?"

Misato nodded. "Afraid so. Turns out that he also had a hand in Second Impact."

"No way..." Shinji muttered. "It can't get any worse."

"It just did," Misato said grimly. "Asuka has joined Seele, and is on her way. We got to get you to the Geofront fast."

At that moment, an ominous shadow covered the sun. Snake looked upward, and saw a massive glider-like bomber overhead. "Too late. She's already here."

* * *

The Geofront, Nerv Headquarters.

The assorted Nerv employees and Patriot operatives watched as the single glider made their way to the downtown area of Tokyo-3.

"Damn," Big Boss cursed. "She's here."

"Who?" Fuyutsuki asked.

Ritsuko answered the question. "It's Asuka. She's piloting Unit Five."

The Nerv faculty went silent at the bottle blonde's proclamation. They knew that Asuka had went missing following her dismissal, but had never thought that she would go to the other side.

"Wait...what?" Maya had said, echoing the sentiments of the Nerv staff.

"Asuka is now working for Seele," Ritsuko explained. "She's after Shinji, as well as acting as backup for the Haven Troopers." She walked over to Otacon's laptop, where he was receiving by-the-minute information regarding the battle above them. "Dr. Emmerich, give me the best route to the Geofront."

Otacon punched in several keys. "They can't go in from Downtown, since most of the firefights are there." He pointed to the screen. "Two of the four freight entrances have been destroyed. There's still the south freight entrance. They can use that, but it will take them the long way around."

"Can't be helped," Big Boss replied. To Ritsuko, he said, "Get Colonel Katsuragi on the line."

* * *

On the streets of Tokyo-3, several of the FROGS had caught up with the speeding Charger.

Five FROGS on motorcycles appear from around the corner, and open fire on the Charger, Meryl forcing Shinji's head down as the rear windshield explodes from the bullets. Thankfully, no one in the car is hurt.

"Stay down!" Meryl shouted at the Third Child.

The redhead pulls out her Desert Eagles - the second one having been outfitted with an extended barrel and scope, and returns fire. She nails the lead biker, who loses control and careens into a second biker. Meryl's rounds also strike the gas tank, causing the bikes to go up in a ball of fire.

Several more FROGS on bikes appeared, swerving around the broken bodies of their comrades. Shinji kept his head down as Meryl fired both Desert Eagles. Two of them swerved out of the way, before returning fire with their own PN-90s. Bullets whizzed passed Misato's head as she came up on a hard turn. The purple-haired colonel turned the steering wheel hard to the left, making the car pull off a Fast and Furious-style drift. The remaining FROGS failed to emulate Misato's driving abilities and ended up crashing into the steel guardrails.

A third squad of FROGS on motorcycles slowed the gap between themselves and the speeding Charger. Meryl fired her guns at their pursuers, killing three of them, but leaving one behind.

Snake saw the last biker coming. He turned to Misato, as the FROG came up on Snake's side. "When I say so, hit the brakes."

"What?" Misato shouted.

"Just do it!" Snake shouted. "That's an order!"

Misato sped up, pushing the car to over 120 miles per hour. As expected, the FROG hit the gas and sped up as well.

"And...NOW!"

Misato braked hard, planting both feet on the break pedal. Thankfully, the passengers had the good sense to buckle up (Shinji buckling up Pen-Pen for good measure). At the same time, Snake shoved his door open. The FROG tried to swerve, but it was too late. It crashed at full speed into the door, literally ripping the door off the hinges, the impact sending the FROG in the air, flipping end over end in a body flip before landing head-first on the asphalt. She did not get back up, as her skull had cracked upon the street. She twitched for a moment before lying still.

Misato took her foot off the brake and hit the gas, swerving around the body.

As the car picked up speed, Misato's phone began to ring. Without taking her eyes off the road, she retrieved it and answered it. "Colonel Katsuragi...yes, sir, Shinji has been retrieved...we're on our way to the South Freight Entrance...hold on."

Misato tosses Shinji the phone. "It's Big Boss."

Shinji answered the phone. "Boss? is that you?"

"Yeah. It's me. Listen carefully, Shinji. Asuka is in Tokyo-3. She is piloting an EVA unit and is on the warpath. She has joined Seele in an attempt to get her revenge on you. She will not stop until you're dead."

"Wonderful. The Red Devil's snapped."

"Yeah, no kidding. You're going to have to face her in Unit One. I'm sorry, Shinji, but there's no other way. You have to stop Sohryuu. I'll see you once you get to the Geofront. Don't worry. You're in good hands."

* * *

Above the speeding car...

The red Entry Plug was loaded into the black-and-red EVA, its armor sliding shut. Seconds later, Evangelion Unit Five was online, its pilot's synch ratio holding at a perfect 100 percent.

Asuka Sohryuu performed the startup procedures inside her entry plug. Rather than her usual crimson Plug Suit, her new Plug Suit is black with red trim, with the number 05 stenciled where the 02 would normally be. Her neural connectors are also black. The look on her face says it all. With the S² Engine inside Unit Five, she has free reign.

She looked down, and saw the speeding black Charger as it swerved through another Haven checkpoint. In an instant, she recognized that style of driving. Within seconds, the profiles of Shinji Ikari, Misato Katsuragi, Meryl Campbell and Iroquois Pliskin (Snake's alias) were on the screen. A sadistic smile spread across her lips as she saw that termination orders were placed on all parties involved.

'I'm coming for you, Shinji,' she thought as she gripped the duplicate Lance of Longinus in her EVA's hand.

The glider then released its cargo, sending Unit Five into a free-fall. It would land in the downtown area, as expected. Afterwards, Asuka could simply track down the Nerv sedan and crush it underneath her heel.

Unit Five flipped in mid air, before landing in a crouch-like position.

But before it could accomplish its mission, it was body-checked by an unseen force, sending the advanced Evangelion to the ground.

RAYs 1 and 3 have come to play. Dropping their stealth camos, they prepare to attack. Asuka watched as the speeding Charger made its escape. The disgraced Second Child rose to her feet, and retrieved the lance.

Asuka had not forgotten that strange mecha that had made a complete fool of herself. She didn't care that there were two of them. All she cared about was that Shinji Ikari would soon see why she was the superior pilot.

"_**I'll take you both on!**_" Asuka howled in her native tongue, just as the two RAYs leapt at her.

* * *

Meanwhile...

The Dodge Charger was out of the city. At the moment, it was on the highway. Shinji recognized the highway as that of the scenic highway, the same one that Misato had taken him following the battle with Sachiel.

Now, as the city was in fortress mode, Shinji watched as Unit Five took on RAYs 1 and. 3. So far, the highway was deserted, as the FROGS had not made it this far just yet. Overhead, Raging Raven flew, flanked by her drones.

Against an EVA armed with heavy artillery, the RAYs had no problem. Against an advanced EVA armed with something as dangerous as a replica Lance of Longinus, that was another story.

Asuka's AT-field blocked RAY 1's water cutter, while RAY 3 attempted to attack her from behind. Not one to fall for the same trick twice, Asuka broke off the AT-field, spun around, and thrusted the Heavy Lance into RAY 3, running it straight through. She then yanked her lance back and with a feral yell, cleaved RAY 3 straight down the middle. The two halves of RAY 3 fell to the streets in a heap, destroyed.

* * *

Nerv Headquarters.

Otacon turned to Big Boss. "RAY 3 has been completely destroyed!"

Big Boss nodded. This certainly was something that he was not expecting. He had thought that all of the duplicate Lances were destroyed when he ordered the attack on the Tarumae Facility. But it was apparent that Zero himself was not without surprises of his own. He had designed the RAYs to withstand gunfire from the EVAs' pallete rifles and rockets. They were not designed to withstand a weapon such as the Lance of Longinus. From the look of things, it could cleave through the RAYs like a hot knife through butter.

"Damn," Big Boss cursed. "I should have planned for this. If this continues, then Sohryuu will destroy RAY 1 in a matter of minutes. What's Katsuragi's ETA?"

"They are approaching the South Freight Entrance, General," Maya replied. "Their ETA is less then five minutes."

"Good. RAY 1 will just have to stall in the meantime until we can get Shinji out there."

* * *

Inside the Charger, Shinji, Snake and Meryl watched in abject horror as Unit Five first impaled, then cleaved RAY 3 in two. Unit Five let out a triumphant roar before it turned its attention to RAY 1, who had fired fired off several missiles. Asuka had deflected them with her AT-field, and tried to perform the same attack on RAY 1.

However, the AIs used to control the RAYs were quick to learn from their mistakes, and RAY 1 simply hopped back in order to avoid Asuka's thrust. One quick blast from the Ion Cannon had knocked Asuka's lance from her hands, forcing the half-German pilot to fight barehanded.

In the meantime, Raven and her drones had rejoined Shinji and the three adults, and just in time too.

"Oh, SHIT!" Misato cursed as they approached the Freight Entrance. Two Humvees with gun mounts, as well as an armored personnel vehicle, along with a squad of Haven Troopers, blocked the entrance. A Haven checkpoint.

Flying overhead, Raven quickly reacted. Her drones fired their rockets at the checkpoint.

**KA-BOOM!**

The Humvees flipped end over end, while the APV was blown to the side, the FROGS themselves sent flying as Misato's Charger and Raven zoomed past, the Humvees crashing to the ground.

"This entrance will take us directly to Nerv HQ!" Misato shouted. "If we're lucky, this should take us to Central Dogma!"

"Then step on it!" Snake shouted.

Up ahead, was another Haven checkpoint. Since the drones had exhausted their rockets, Raven zoomed ahead. Brandishing her grenade launcher, she fired six grenades at the Haven checkpoint. The Humvees were blown to the side, the Charger and Raven sped past the destroyed checkpoint.

"Good work, Raven," Snake said on the CODEC. "You're needed in the Geofront. Backup the JSSDF and Wolf."

"Roger that," Raven replied as she joined the battle alongside Wolf and the JSSDF.

* * *

Nerv Headquarters, the Bridge, minutes later.

Following Makoto's directions, Misato, Shinji (holding Pen-Pen), Snake and Meryl had avoided the ares where the major firefights were taking place, and had reached the bridge. Along the way, they had ran into several stray FROGS, but there were quickly disposed of by Misato, Snake and Meryl.

"Big Boss!" Shinji shouted as he released Pen-Pen, happy to see that his mentor was still alive. Pen-Pen, in the meantime, had waddled off to where Maya sat and hid under the console.

Big Boss turned to his student and smiled. "Glad you could make it, kid," he said. He turned to the screen, where Asuka had just destroyed one of the RAYs with the Lance. "There's no time, Shinji. Unit One is ready. You have to stop Asuka."

Shinji nodded. "I know."

"From what we know," Big Boss continued, "Unit Five is an advanced prototype. Like your Unit One, it also has an S² engine. What makes it more dangerous is that is armed with a duplicate Lance of Longinus. The Lance is powerful enough to penetrate the even strongest AT-field. The Lance has two forms: a heavy spear, which can morph into the Lance. So be careful."

Shinji nodded. "Got it." He then looked around. "Wait...where's Rei?"

"She's not in her Unit Zero," Ritsuko said. Then a dreadful thought came to her. Rushing over to Maya's console, she typed in several keys. Within seconds, Rei's image was on the screen. She was standing in front of the destroyed Reiquarium. "She's in Terminal Dogma!"

"What the hell is she doing down there?" Misato asked.

Ritsuko pointed to the screen. Gendou Ikari had appeared.

Big Boss looked at the screen. "He's going to try and initiate Third Impact," he said.

* * *

Terminal Dogma.

Gendou had made it back to his office. There, he had taken his hidden elevator straight to Terminal Dogma.

Rei wasn't hard to find. She stood in front of the destroyed Dummy System, looking at the remains of her clones inside the Reiquarium.

"I thought you would be here, Rei," Gendou said as he stepped out of the shadows.

Rei remained silent as she turned to Gendou.

"It's time. The promised moment is upon us. Let's go."

Silently, Rei followed Gendou deeper into Terminal Dogma.

* * *

Central Dogma, the Bridge.

Ritsuko punched in several keys. On the far side of the bridge, a hidden elevator activated. "Okay, I've activated Emergency Elevator R-10-20. We can drop Shinji off at the EVA Cages, and we can head for Terminal Dogma."

Misato reloaded her pistol. "Sounds like a plan. Let's go, Shinji."

Shinji nodded and followed the two most powerful women in Nerv to the elevator. However, as he reached the elevator, he stopped.

Turning to the three bridge bunnies, he simply said, "Sorry for blowing up at you three," before joining Misato and Ritsuko inside the elevator.

As the doors closed, despite the circumstances they were in, the three bridge bunnies smiled.

* * *

EVA Cages.

Unit One was placed on the lift. Shinji Ikari was inside the Entry Plug. He had no time to change into his Plug suit, given the severity of the situation. Misato had handed Shinji his neural connectors as he exited the elevator before the elevator continued on to Terminal Dogma.

Big Boss' image appeared before Shinji. "Okay, Ikari. We're going to send you close to Asuka's location. Reports are coming in that she had just destroyed RAY 1. You have to stop her before she can reach the Geofront."

"Understood," Shinji replied.

"I'm sorry it has to be this way, Shinji," Big Boss continued, "But we have no choice."

Shinji nodded. "I know, Boss."

"The techs have added a second Progressive knife in your other shoulder pylon," Big Boss continued. "Remember what I taught you about weapons combat?"

"Yes, sir."

"Good to know. You turned out to be one of my best students. The best way to render the EVA immobile is to destroy the core, since its core can repair and regenerate most injuries. Godspeed, Ikari."

Big Boss then ended the call.

* * *

Somewhere in Central Dogma...

The last Haven Trooper fell to her knees, her heart sliced in two by Raiden's high frequency blade. The White Devil kicked her lifeless corpse over as he wiped the blood from his blade.

Then his CODEC came to life.

"Raiden here."

"It's Snake. Where's your location?"

"Near Commander Ikari's office."

"There's a hidden elevator inside the office. Otacon's activating it now. Head down to Terminal Dogma and backup the good doctor and Colonel Katsuragi. When you're done there, return to Central Dogma."

"Understood," Raiden replied, and the call ended.

Three more FROGS charged from around the corner, guns drawn. They opened fire on Raiden, who simply deflected the bullets with his sword. The first FROG lost her head, while the remaining two were left to bleed to death after losing several appendages.

Raiden found Gendou's office and entered. At the far wall, there was an open passageway, revealing a lift leading down to Terminal Dogma. Raiden boarded it and was on his way down.

* * *

In the streets of Tokyo-3, RAY 1 had been literally torn apart. Asuka had been expecting to find a human pilot inside, Only to find that the RAY was completely unmanned.

"_**What?**_" Asuka gasped. "_**Where's the pilot? Is this thing unmanned, like Jet Alone?**_"

Her chain of thought was interrupted when warning klaxons were heard coming from a nearby hatch. Asuka saw that the hatch was opening, meaning that soon, either Unit Zero or Unit One will come to play.

Her Lance was nearby, so Asuka quickly retrieved it. Rushing over to the opening hatchway, Asuka prepared to cleave the offending EVA, not giving it a chance to be released from its restraints.

The hatch opened and Asuka drew the lance back.

With a loud screech, the lift came to a halt...

...only problem was that there was nothing on the lift. No EVA. Nothing. Only one word was painted at the bottom of the lift. Given Asuka's problems with reading Japanese Kanji, it took her a moment to realize what it had said.

**SUCKER.**

"Hey, Sorhyuu!"

**WHAM!**

Asuka felt herself being launched several feet down the street as she was struck from behind, the lance falling from her hands as she slid down the street.

Unit One dropped the 'flipper' of the destroyed RAY. Big Boss had suspected that Asuka would have been waiting for him to ambush him, so he simply caused a diversion.

The location Asuka was at had a second hatchway. While Asuka was distracted with the first one, the second hatchway opened, and Shinji came through in Unit One, having climbed to the surface..

Seeing that Asuka was distracted, Shinji quickly capitalized on his good fortune. He grabbed the destroyed RAY's flipper, snuck up behind Asuka, and with a giant swing that would have made a major league slugger proud, smashed Asuka in the back with the flipper.

Unit One dropped the flipper and activated the first Progressive Knife. He then activated his visual of Asuka. "Looking for me, Sohryuu?"

Asuka got to her feet and turned around. She retrieved her Lance. "_**So...the coward finally shows himself.**_"

Shinji frowned. "I can't speak German, idiot. Speak in Japanese."

Asuka growled. "I said that you finally show yourself, you coward."

"That's rich, coming from someone like you," Shinji retorted, ready for when Asuka would attack. "The great Asuka Sohryuu was more than willing to send mankind to oblivion because you wanted to be the best."

"I AM THE BEST!" Asuka screamed. "KEEL CHOSE ME! HE CHOSE ME TO PILOT UNIT FIVE! I AM THE SUPERIOR PILOT! NO ONE IN NERV WOULD UNDERSTAND THAT! ALL THEY GO ON IS ABOUT THE GREAT SHINJI IKARI, THE KILLER OF ANGELS! THAT TITLE SHOULD BE MINE!"

"You don't get it, do you?" Shinji retorted. "I never wanted to pilot the EVA! I never wanted the 'Killer of Angels,' title! I just wanted a normal life. But life is never fair, Sohryuu."

"Spare me your sympathy," Asuka snarled.

"I'm not offering any. Answer me this question, Asuka. Why? Why did you do what you did to me?"

Asuka's voice was like ice. "Because I refuse to lose to a spineless little bastard like you. I am the superior pilot. Not you. Not Wondergirl. You should have just stayed gone inside your unit's core, Shinji. You should have stayed inside the core, and I would be the savior of humanity." She twirled the Lance. "Looks like I'll just settle for killing you."

Shinji's grip tightened on the knife. "You can try."

The two EVAs faced each other in a Mexican standoff. Then they both charged.


	10. Episode 9: Battle For Humanity, Part 2

_**Episode 9: The Battle for Humanity! Seele vs. The Patriots, Conclusion**_

Snafu's Notes: Try not to misunderstand. The story will not be complete until I post the Epilogue. The chapter was just too damn long (30 pages!), so I split it in two. Fixed the typo with Gendou and some minor details.

Terminal Dogma.

Gendou Ikari and a nude Rei Ayanami stood before the massive form of Lilith, crucified, the Lance of Longinus impaled in her body. Above him, in Central Dogma and the fortress city of Tokyo-3, the battle for humanity continues to rage on. Upon hearing that Shinji was fighting Asuka, he realized that the Section 2 agent had failed in her task.

'No matter,' Gendou thought as he removed his glove, revealing the grafted embryo of ADAM. 'I have waited ten years to be reunited with Yui. Nothing can stop me.'

He looked at Rei. "It's time. I am one with ADAM. This is the only way to meet with my dear Yui once again. The forbidden union of ADAM and Lilith..."

At that moment, Rei's left arm fell, as if it had been severed above the elbow, bone exposed. What was surprising was that there was no blood.

"Your AT-field can no longer maintain its shape," Gendou continued. "Open your AT-field, Rei...open the barrier of your heart. He raised his hand with the grafted Angel. "Leave your useless body, my little doll, and release your soul. Merge all the souls into one, and take me to Yui's side."

Gendou was expecting to sink his hand into Rei's body, thus triggering his version of Third Impact. What he did not expect was the blue hexagonal field that erupted between himself and Rei, effectively putting a stop to his plans.

An AT-field.

As Gendou watched, the arm had dissolved into LCL, while Rei used her newly awakened S² organ to regenerate her lost arm.

"I...am not your doll," Rei rebuked, using the force of the AT-field to knock Gendou on his ass. "As you can see, I can maintain my form just fine. Everyone has their destiny," Rei said as she stood over Gendou flexing her regenerated hand. "My path lies not with you, but with your son."

"You..." Gendou sputtered. This was something he was not expecting. "You dare choose him over me!"

"I will not help you initiate Third Impact," Rei said. "Your hands are already stained with the blood of the people you killed in Second Impact."

"I...I made you to serve my purpose!" Gendou snarled as he rose to his feet, now completely mad. "My purpose! I don't care if I have to kill every last person on this base, let alone this planet! I will be reunited with Yui!"

"That is not love," Rei rebuked. "That is obsession."

"You can't love! You will serve your purpose to me, and deliver me to my wife!"

With a burst of speed, Gendou charged at Rei, preparing to thrust his hand containing the progenitor of the Angels into her body, thus initiating the forbidden union of ADAM and Lilith, but more importantly, triggering Third Impact, and more importantly, instrumentality.

Before Rei could raise her AT-field to defend herself from Gendou, she heard the unmistakable sound of live steel being drawn, which was followed by...

**SLASH!**

**THUMP.**

Gendou's hand and arm fell to the floor, severed at the elbow.

Time had stopped for both the deposed commander and his former doll. Rei turned to her savior while Gendou was looking at the bloodied stump, shock overriding the pain.

Raiden turned around, high frequency blade in his hand, stained with Gendou's blood. Turning to Ritsuko and Misato, who and rushed in after Raiden's crude amputation of Gendou's arm, he said, "Orders from the old man. You two clean up here. I'm needed topside," right before leaving through the same passageway that Gendou had entered from.

Gendou looked at the stump, then at his severed arm, still in complete shock as to what had happened. "Wh-what?" Then the pain kicked in, as the bloodied stump began to spray out blood. "MY HAND!"

As Gendou screamed in agony, the bottle blonde scientist and the lavender-haired major rushed over to Rei. "Rei! Are you all right?" Misato asked, while Ritsuko handed Rei her lab coat.

"I am fine," Rei replied as she slipped the lab coat over her naked body. "What is happening?"

"Seele has invaded the Geofront and the city," Ritsuko explained. "Shinji is fighting Asuka in Tokyo-3 and we need you to pilot Unit Zero and help the JSSDF inside the Geofront."

"Understood," Rei acknowledged.

"TRAITORS!"

Gendou's scream had the desired effect. The two most powerful women in Nerv spun on their former commander, who had his gun out with his remaining hand.

**BLAM!**

Gendou looked at the hole in his chest, then at Misato, who already had her gun out. The H&K P8's barrel was smoking, following Misato firing it at Gendou. With a yell, Gendou raised his gun again.

**BLAM!**

This time, the bullet struck Gendou in the lung. He looked at Ritsuko, the older woman having retrieved her own gun, the same make as Misato's, the barrel still smoking, the spent round falling to the floor.

Gendou screamed again as he tried to raise his gun once more. But he would not get the chance to fire, since both Misato and Ritsuko opened fire on the one-armed man. This was more than just an execution. To them, it was personal. Through Gendou's machinations, Ritusko's mother was driven to suicide and Misato's father died while saving her life. Those who had died in the maelstrom of Second Impact had demanded justice, and it was Misato and Ritsuko had delivered, acting as Gendou's executioners. One of the bullets fired from Misato had punctured his back, destroying his spine, leaving him paralyzed from the waist down.

Gendou fell to the floor, blood seeping from his bullet-riddled body. In the face of his own death, he realized that he had failed. He would not see Yui again.

The dying man looked at Rei, who in his mind's eye, shifted into Yui. With his wife's name on his lips, Misato fired one final bullet into Gendou's head, while Ritsuko emptied her last few bullets into ADAM. ADAM's corpse dissolved into LCL, where it seeped through the metal catwalk and into the LCL lake.

With the death of Gendou Rokubungi Ikari and the final destruction of ADAM, Third Impact was successfully averted. Humanity would survive.

Ritsuko and Misato turned from the grisly sight. Rei had watched the execution with her usual stoic expression. "If you are finished here, we must hurry to the EVA Cages. I take it that Unit Zero is ready for sortie?"

Misato nodded. "We should go." She gestured to the bullet-riddled corpse of what was Gendou Ikari. "He's not going anywhere."

Ritsuko nodded. The two adults and the teen left Terminal Dogma.

* * *

Above ground, in Tokyo-3...

(We see the following caption in English and Japanese: **Tokyo-3: Downtown.** The Encounter [Boss Theme] Theme from MGS1 is playing.)

Two massive behemoths squared off in the deserted streets of Tokyo-3. One was a black and red-trimmed Evangelion - an advanced prototype - cloned from ADAM's DNA, its pilot a disgraced Evangelion pilot, while the other was a mostly purple Evangelion - the test type - cloned from the DNA of Lilith, its pilot the son of the late Gendou Rokubungi Ikari.

Unit Five charged at its opponent, who stood its ground, armed only with a Progressive Halberd. Lighter, but lacking the range and power of the Heavy Lance.

Dodging Unit Five's wild swings with the Lance, the two EVAs ended up locking weapons, Samurai Shodown-style. After a moment, Unit Five knocked Unit One away, its only saving grace was that it tripped over one of the split halves of RAY 3, falling on its back, just as Unit Five made an attempt to decapitate Unit One.

Asuka cursed as Shinji's Unit fell. Oh well. She wanted to make him suffer, anyway. Maybe chopping the EVA's limbs off piece by piece would suffice, right before chopping off its head. Oh, was Shinji going to suffer for making her look like a complete amateur. Unit Five leapt into the air, preparing to impale the downed EVA in its shoulder.

Unit One rolled out of the way, narrowly missing being ran through by the Heavy Lance. However, this turned out to be a blessing in disguise, as Asuka had miscalculated the force used in her strike, the Heavy Lance being impaled into the pavement.

The test-type Evangelion got back to its feet, grabbing the Halberd. Holding it like a Louisville Slugger, Unit One cocked it back and swung with all its might. The flat side of the Halberd's blade connected with Unit Five's head, knocking it away from its Lance, which Asuka had been trying to retrieve, with little success. Unit Five tore out huge chunks of pavement as it slid down the street.

Inside the cockpit, Shinji had switched over to sound only. Right now, he was hearing Asuka screaming choice curse words in Japanese and German as she got to her feet.

"Damn you, Ikari!" Asuka shouted. "I'll see you dead!"

Shinji knew that Asuka was playing for keeps. Had he been the same now as he had been during the battle with Bardiel, he would have more than likely let Asuka kill him. Too bad for Asuka. The old Shinji Ikari was gone.

Shinji saw that the Halberd's blade was destroyed, thus rendering the weapon useless. He dropped the weapon, the handle falling next to two abandoned big rigs, each with a tanker trailer.

Both tanker trailers were was at the moment, full of gasoline.

Shinji had a moment in inspiration. If gasoline was flammable, what would happen if it a tanker filled with the stuff came into contact with an AT-Field?

Unit One picked up the first tanker.

Unit Five charged at Unit One, who quickly tossed the impromptu grenade at the former. By reflex, Asuka had brought up her AT-Field.

**BOOM!**

The tanker detonated on impact, the flash temporary blinding Asuka, who was once again, screaming in Japanese and German.

As Shinji reached down and picked up the second tanker, a weapons locker rose from the ground. Inside, was a Mag-Rifle. Shinji quickly retrieved it. Looking bak at Asuka, who was still blinded from the first blast, her Unit Five holding the 'eyes' with one hand, while trying to reach out with her other hand.

Unit One tossed the second tanker at Unit Five. Then, as it neared Unit Five, Shinji took aim and fired.

**BAM!BAM!BAM!**

**BOOM!**

The rounds found their mark, the tanker detonating like a bomb.

Inside Unit Five, Asuka screamed as she felt the pain on her right arm. It was as if her arm and hand were on fire. Tearing off the sleeve of her plug suit, she saw that her forearm and hand were covered in first and second-degree burns, a side effect of her high synch ratio, now in the lower 200s.

At least the LCL inside the Entry Plug helped ease the pain...somewhat.

Shinji wasn't finished yet. He unloaded the Mag-Rifle as he charged, but Asuka's AT-field spared her from further damage. Shinji's AT-field canceled out Asuka's own field, allowing Unit One to shoulder ram the advanced prototype, knocking her to the ground.

* * *

Inside the command center...

Big Boss' continued to monitor and direct the JSSDF and UN forces inside the Geofront. Earlier on, the two forces had fought to a standstill. Now, the news looked even more promising.

The Haven Shock Troops were taking on massive losses inside Central Dogma, the tight corridors being their major disadvantage, as they were used to be even more mobile. It looked even more grim for them outside in the Geofront. The combined forces consisting of the U.N. crack troops, the JSSDF and the Beauty and Beasts Corps were hammering the forces back.

Naomi was on the phone with Misato. "That's good to hear. I'm glad she's okay. And what about Ikari?"

"Dead. I executed the bastard myself. Ritsuko took care of ADAM. We're inside the EVA Cages. Ritsuko and I will remain in the cages until the heat dies down. Terminal Dogma is locked down."

"Smart move," Naomi replied. "Haven forces have been taking on heavy losses. We're pushing them back. We can hold out until the more soldiers from the U.N. arrive, but it's going to be close."

"That's great news!" Misato rejoiced. "Rei should be finishing up getting into her Plug Suit, so she can help the good guys out in the Geofront. How's Shinji?"

Naomi looked at the screen. The fight between Shinji's Unit One and Asuka's Unit Five continued to rage in the streets of Tokyo-3.

"He's holding his own at the moment," Naomi reported. "Big Boss taught him well. I'll let the old man know where we stand with Ikari."

Ending the call, she walked over to Big Boss, who was standing with Snake and Meryl. "Good news from Terminal Dogma, Boss. Rei is safe. She is being prepped in Unit Zero as we speak."

"And Gendou Ikari?" Big Boss asked.

"Dead. Misato killed him herself. Akagi destroyed ADAM. Third Impact is no longer possible. Ritsuko and Misato will stay at the EVA Cages until that area is secured."

Big Boss nodded. "Good. Very good. The U.N. just notified me that extra troops will be arriving in Tokyo-3 shortly. All we got to do is..."

He was cut off as one of the JSSDF soldiers yelled out "Contact! Bottom Level!"

Big Boss pulled Naomi to the floor as gunfire erupted, the bridge bunnies and the two Patriots operatives following suit. Snake pulled Meryl to the ground as bullets whizzed by them The Haven Troops had made their way to the command center, although it was the bottom half, the same level Hyuuga showed up in warning about Matrarel's attack during the power outage. The JSSDF troopers on the bottom level returned fire, but the Haven troopers had brought in riot shields, allowing their teammates to return fire.

What they did not expect was Big Boss himself on the command bridge.

Brandishing his Patriot, Big Boss joined in the fray, as did the rest of FOXHOUND and Kaji, while Otacon and Mei Long continued to keep low and monitor the battle, Naomi was tending to Maya, who was starting to hyperventilate. Deciding that Maya was a threat to herself, Naomi produced a syringe, containing the knockout serum used on Ritsuko and jammed the item into her neck.

Maya was out like a light.

Armed with a carbine with a grenade launcher attachment - a memento from the Big Shell Incident of 2009 - Snake returned fire, provoking the FROGS to hide behind their shields. Then he fired off a grenade from the underhand attachment. The ensuing explosion sent the first wave flying.

Before the defenders could get a breather, a second wave of FROGS came storming in through the open doors. This time, Hyuuga was hit in the arm from the second barrage of gunfire. As Naomi treated the bespectacled male bridge bunny's injury, Kaji scored a headshot on one of the FROGS who had peeked from behind the shields.

Four of the FROGS leapt up onto the same tier as were the Patriots from their place below. One of the leveled her PN-90 at Big Boss...

**BLAM! BLAM! BLAM!**

...only to have Meryl make the save. Three rounds from the redhead's Desert Eagle had sent the first FROG flying off the upper level, and back onto the bottom level below.

Two of them went after Solid Snake. Brandishing machetes, they closed in on the son of Big Boss. Snake parried the first machete swing, and fired off a burst into the first FROG, the armor-piercing rounds going through the FROG's heart, killing her instantly.

The third FROG kicked the carbine out of Snake's hand, forcing the FOXHOUND commander to pull out his CQC Knife. Snake parried several of his opponent's machete swings, right before jamming the knife into her throat. He then pulled his knife out and kicked the woman off the tier, sending her body down to the bottom ramparts below.

Big Boss, in the meantime, tossed the Patriot at Kaji, and went after the remaining FROG. Within seconds, the FROG fell dead, her neck snapped by the surprisingly strong old man.

More FROGS appeared on the bottom tier, forcing the defenders to take cover from the intense hail of gunfire. Just as it appeared that the command center would be overrun, the good guys got some good news.

"Big Boss! I got movement!" Mei Ling shouted a she looked at her laptop. Her face then lit up as to what was coming. "It's Unit Zero!"

**CRASH!**

Just as Zeruel had done when he invaded the Geofront, Unit Zero had crashed through the walls of the command center. The single eye of the Prototype-model Evangelion looking down on both the Patriots and the FROGS.

Inside the Entry Plug, Rei Ayanami – in her Plug Suit – quickly amassed the situation, as the FROGS opened fire on her. The bullets did nothing against Unit Zero, as it slammed its hand onto the tier, knocking several of the FROGS over, right before sweeping its hand left to right, killing the remaining invaders. One punch to the bottom tier's doors had effectively sealed off the bottom half of the center from further attack.

"All right, Rei!" Kaji shouted.

Unit Zero gave a small salute to the cheering defenders before leaving to assist the JSSDF and UN troops outside the Headquarters.

* * *

Above ground...

Asuka Sohryuu was not very happy.

Despite having the better EVA, she had clearly underestimated Shinji's resolve. Things had went downhill quick. Despite being armed with the duplicate Lance of Longinus, as well as having trained in the EVA for most of her life, Shinji Ikari has once again, proved that he was better than her.

"It's over, Asuka," Shinji deadpanned. "I've gotten word that your Haven buddies are getting their asses kicked in the city and inside the Geofront. You're finished."

"NO! YOU'RE FINISHED, IKARI!" Asuka screamed as she grabbed the embedded lance and literally **yanked** it out of the ground. She then cocked her arm back and heaved the Lance blade-first towards Shinji. "DIE!" she screamed.

Shinji's reaction was instant. His AT-field had appeared, stopping the weapon in mid-air.

Then the weapon changed. From a heavy-looking lance to its true form. A spear-like weapon, the end facing Shinji morphing into massive twin tines.

Shinji dropped his AT-field and dodged the lance, the lower tine nicking his arm as it sailed past, impaling a nearby weapons locker. As he dodged, Shinji activated his second Prog Knife and hurled it blade-first at Asuka.

Asuka saw the knife coming, but she was a split second too late in raising her AT-field. The knife found its mark, impaling the left eye of EVA Unit Five. Unfortunately, for Asuka, given her high sync ratio, it had severely damaged her own eye, the feedback rupturing the eye. The EVA mimicked Asuka's movements as both the EVA and Asuka screamed in pain.

After a moment of this, Asuka yanked the knife out of her EVA's eye. "I'll kill you...I'll kill you...I'll kill you...I'll kill you...I'll kill you...I'll kill you...I'll kill you all," she chanted as she reached behind her flipped open a hatch. Unlike the Japanese kanji she had a problem with, this was in a language she could easily understand – German.

Translated it read, **D-DRIVE**.

Asuka had planned to use the self-destruct sequence to destroy herself, Shinji, and all of Tokyo-3.

Shinji had a video feed into Asuka's plug and saw what she had intended to do. He looked to his left, and saw that he had rolled near a second weapons locker, having been raised from the ground. Among the items inside, was a Progressive Naginata, a prototype weapon that Ritsuko and R&D were developing shortly before Zeruel. Shinji yanked it out of the weapons locker, took aim, and threw it.

Shinji's throw was true. EVA Unit Five was impaled through, the core pierced completely, thus neutralizing the self-destruct sequence. However, it wasn't over just yet. As a result of Shinji throwing the naginata, Unit Five had automatically ejected its Entry Plug in order to save its pilot's life.

Unit Five fell to the ground, the lance still sticking out of its midsection, the core destroyed.

* * *

Back inside the command bridge, the JSSDF had moved in, securing the area. Rei - in her Unit Zero - had drove the remaining FROGS to surrender. Being the pilot of a humanoid fighting machine armed with a 100-round Gatling Gun sure did worked wonders. During this time, Misato and Ritsuko had returned to the command center once the area was secured.

The battle in the Geofront and in the city above was indeed brutal. The Haven Shock troops were not expecting the full brunt of the JSSDF bearing down on them, nor the backup from the U.N. crack troops or from the Beauty and Beasts Unit. The Haven forces had suffered devastating losses.

Aoba turned to his console. His expression then lit up. "Commander Fuyutsuki! I got U.N. troops advancing through the Goura perimeter!"

Hyuuga's face mirrored that of her male counterpart. At least the painkillers Naomi had were working. "I got two more JSSDF and U.N. combat units approaching from Gotemba! They're pushing their way through the FROGS' defense perimeter!"

Maya – who had just returned to consciousness moments earlier – turned to Fuyutsuki. "The FROGS have been pushed out of Nerv Headquarters. They are surrendering to the JSSDF and U.N. forces!"

Fuyutsuki smiled broadly, watching as the others cheered, reveling in their victory. Ed and Johnathan butted heads, while several of the JSSDF soldiers who had survived the assault fired their guns into the air. Even Snake and Meryl got into the celebration. Meryl grabbing Snake by his flak jacket and kissing him full on the lips.

"So how does it feel to be a hero, Dave?" Meryl asked.

Snake smiled. "I'll get back to you on that."

Kaji, in the meantime, had removed his flak jacket. He had caught a round from the FROGS' assault Thankfully, the jacket did its job and stopped the bullet.

The ponytailed man the felt someone grab his shoulders and forcibly spin him around. Before he could say anything, Kaji was caught in a liplock with Misato Katsuragi.

"Er...does this mean we're back together?" Kaji asked.

"Shut up and kiss me, you jerk," Misato ordered.

Kaji smiled. "I love it when you're pushy."

As the Patriots spy and the Tactical Operations Director kissed yet again, Big Boss approached Snake and Meryl. The old man had a smile on his face as he approached the pair.

"Son," Big Boss said.

"Dad," Snake replied.

The two shared a handshake. Big Boss turned to Meryl. "Major Campbell. Your father would be proud of you. I know I am."

Meryl beamed from the praise. "Thank you, Big Boss."

Meanwhile, Kouzou Fuyutsuki let out another sigh of relief as he sunk deeper into the chair. "It's over."

Ritsuko shared his sentiment. "Thank God."

"Not yet," Big Boss replied as he turned from Snake and Meryl. "Sohryuu is still on the loose."

"We got a signal from her Entry Plug," Ritsuko said. "Shinji is on his way to it now."

* * *

(Once again, the following appears in English and Japanese: **Tokyo-3: Lake Ashinoko**.)

Since every Entry Plug was equipped with a homing beacon for other Evangelion pilots in the event that they were forced to eject from their Evangelions, it was easy to track down Asuka's entry plug. It had came to a stop on the beach of Lake Ashinoko.

It was also empty, as Shinji had noticed upon further inspection, upon ejecting his own Plug and exiting from his EVA. The only sign of life was that of an open first-aid kit, obviously LCL-proof.

'The hell?' Shinji thought. 'Where the hell is Asuka?'

His unspoken question was answered when Asuka grabbed him from behind, slammed him into the side of the Plug, right before throwing him to the ground. She then followed with a swift kick to the torso, knocking Shinji on his back.

Asuka was on top of Shinji, her hands on his throat, choking the life out of him. Shinji had saw that his Progressive Knife to the left eye had pretty much ruptured Asuka's left eye, the end result of having such a high synch ratio. Her damaged eye was heavily bandaged (as it was in End of Evangelion), as was her right hand.

"You and I...got a score to settle, Ikari," Asuka sneered. Her grip increased on Shinji's throat. "You took everything from me! Everything! I was the best pilot! Number one synch ratio! I am superior! This is it for you!"

In desperation, Shinji slammed his palms on Asuka's head, causing her ears to ring painfully, which gave Shinji the opportunity needed to get her off of him. He kicked her off and rolled backwards, giving himself some room from the half-German sociopath, taking in deep breaths of air.

The two pilots faced off, the bleeding from Asuka's eye slowed down, while Shinji shook off the effects of Asuka's sneak attack.

Then, much to Shinji's surprise, Asuka shifted into a CQC stance. "So you want to do things the hard way, then?" she taunted. "Fine. I won't need an EVA to beat you!"

Shinji stood up and went into his own stance.

The final battle between the two had begun.

Shinji lunged in with a punch, only to have Asuka grab him and slam him to the ground. He got back up, and measured Asuka again. Once again, he found himself on the ground, Asuka having slammed him yet again when he tried to kick her, Shinji rolling away when she tried to kick him in the nuts.

This time, Asuka tried to attack Shinji with a straight punch to the face, only this time, Shinji slammed her to the ground. They both locked up, wrestling-style, with Asuka gaining the advantage by flipping Shinji over, landing in the surf. Shinji countered with a Krav Maga-style take-down on Asuka.

The battle between the disgraced Second Child and the Third Child continued.

* * *

Nerv Headquarters, the Geofront.

From a UAV drone, Big Boss and the others saw the battle between Ikari and Sohryuu. 'So...Sohryuu's been training with the Haven Shock Troops,' he thought.

For the past several weeks, as Asuka was training inside her EVA, she was also trained in advanced close-quarters-combat. Fortunately, so was Shinji prior to Big Boss' departure to Haruna, so Shinji was holding his own. The real question was for how long.

"I got a lock on their location!" Maya shouted. "It's Lake Ashinoko!"

Big Boss turned to Kaji and Misato. "The both of you, go. I will alert a squad of U.N. soldiers and tell them to meet you there."

* * *

The final battle between Shinji Ikari and Asuka Sohryuu continued. And it was indeed brutal.

The waters had washed away the LCL, leaving both fighters soaked to the bone as they fought in the surf.

Shinji, playing it smart, had moved away from the waters, lest Asuka would try and drown him there when she had the chance. Another countered punch had his arm twisted behind him in an arm bar. Shinji then elbowed Asuka in the face, forcing her to let go. As she staggered back, Shinji waded into her, Asuka blocking his kicks to her torso and head with her free hand as she held her injured eye with the other.

Shinji feinted a kick to the head, and went low, gut-punching Asuka. She responded by grabbing him and slamming him face first into the side of her Entry Plug. After nailing Shinji in the ribs and lower back, she spun him around, only to have Shinji counter by reversing their positions, Shinji bashing her head into the side of the Plug, before throwing her to the ground.

As he went in for the kill, Asuka scooped a handful of sand and threw it into Shinji's eyes, blinding him.

With a feral yell, she tackled him to the surf and rained down blows upon his face, until she was certain that he was unconscious.

"You're nothing compared to me! I'm gonna kill you, Shinji," Asuka snarled as she slugged him yet again for good measure. She then leaned forward, so that she could whisper softly to him.

That turned out to be a huge mistake on Asuka's part. Shinji was playing possum.

"I'm going to kill you, Shinji, and I am so going to enjoy i-**YEEEARRGH!**"

_'A true soldier does not rely on just brute force alone. War is always and will ever be based on deception.'_

Too bad Asuka did not read _The Art of War_.

As Asuka whispered to him, Shinji reached out and dug his thumb into Asuka's injured eye, causing the girl to scream from the pain, as fresh blood to spill out, which was followed by a punch to said injured eye, forcing Asuka off of him, and giving him some breathing room. He splashed his eyes with the lake water, rinsing the sand from them. His lip was busted, and he was bleeding from a cut to the side of his head. On top of that, he was sore all over.

Shinji went back into his CQC stance.

_'Shinji, remember the basics of CQC.'_

Big Boss' words came to him again as he watched Asuka warily. He shifted his stance, lowering his arms slightly, and waited for the attack.

Asuka tore off the makeshift bandage. Her eye was now closed, blood seeping out of the ruptured socket, as if she was crying tears of blood.

'I'm not gonna run away,' Shinji chanted in his mind. 'I can't run away. I WON'T RUN AWAY!'

Now Shinji was on the offensive. Asuka screamed at him and charged, preparing to grapple him into submission. That plan was derailed as Shinji kicked her in the gut, knocking the air out of her torso, followed by a punch to the face, knocking Asuka back, blood flying from her mouth, landing onto the sand.

Shinji was in the zone. Adrenaline pumping throughout his body, dulling the pain, he continued to fight as Big Boss' words came back to him.

_'If the opponent blocks high, hit low. If they block low, hit high.'_

Shinji did just as that. Asuka blocked her face, he nailed her in the torso. She tried to block her mid-section, only to have Shinji strike her in her face repeatedly.

Left cross. Right uppercut. Roundhouse kick. Asuka fell to the surf in a heap. When she tried to get back up, Shinji drove his elbow into her back, causing her to cry out in pain. Asuka rolled out of the way and managed to sweep Shinji off his feet, knocking him on his back.

Shinji rolled out of the way as Asuka tried to stomp his head in. He quickly scrambled to his feet, and sent Asuka spinning to the sand with a roundhouse kick to the head.

Asuka tried once again to throw sand in Shinji's eyes, but Shinji turned his head away, the sand impacting the back of his hair. She then tackled Shinji to the ground, only to have Shinji kick her off of him after blocking several of her blows with his forearms.

Asuka blocked several of his punches and countered with her own combination. Shinji blocked those as well, before punching Asuka square in the face yet again, followed by a kick to her torso, knocking the breath out of her body. Asuka's legs buckled from under her, and she fell to her knees.

Her body felt like it was restrained by weights. But she shakily got back to her feet. Shinji did the same, his body feeling the same as Asuka's.

**CRACK!**

Both Shinji and Asuka's fists impacted on the other's jaws, knocking them down to one knee. The fight was slowly winding down to see who could last the longest.

They stumbled back to their feet.

Asuka struck Shinji. Shinji struck Asuka. Shinji struck her again, causing her to stumble. She fell forward, spitting out blood. She looked at Shinji with her good remaining eye, the damaged one still seeping out blood. "Why...WHY CAN'T YOU LET ME WIN?" she screamed.

She got to her feet. Shinji balled his hand into a fist, ready to deliver the knockout blow. Asuka did the same.

Asuka charged. Shinji held his ground.

Asuka swung...and missed. Shinji had simply ducked under her wild swing.

With a yell, Shinji swung his own fist...

**WHAM!**

...and connected.

Asuka stumbled back several steps. Then she keeled over. Looking at the noon sky, the last thing she thought before slipping into unconsciousness was, 'How disgusting.'

The battle was finally over. Asuka Langley Sohryuu, the pride of Nerv Germany, former prodigy of Unit Two, was defeated.

Shinji turned from the defeated half-German. His whole body was hurting all over, and he could have swore that one of his fingers was broken.

"...inji...Shinji!"

Shinji collapsed to his knees. He would have fell over, but Misato and Kaji were there, the former catching her ward in her arms. Meanwhile the squad of troops had surrounded Asuka. Both parties had arrived in time to see Shinji land the knockout blow on Asuka.

Shinji looked at Misato. The pain was finally starting to get to him. "Did we win?" he asked.

Misato nodded.

"Good. I'm gonna...lie down for...a while."

With those words, Shinji Ikari passed out in Misato's arms.

* * *

It has been three hours since U.N.'s military wing has moved into Tokyo-3 and the Geofront. The people had emerged from the shelters, taking in the carnage that surrounded them. Those that had lost their homes in the war would be reimbursed by the Japanese government. Tokyo-3 will rebuild. Out of the five combat units, only less than two hundred soldiers of the Haven Shock Troops had survived the battles. They would be shipped off to the World Court in The Hague.

Shinji was rushed back to Nerv Headquarters, as was Asuka, under heavy guard. She would be treated for her injuries before being taken to Nerv's detention cells, where she would wait until she was shipped off to Tokyo-2 to face her crimes. Shinji, on the other hand, was in a mini-coma of sorts, but his condition was stabilized. Rei remained at his side.

Gendou's body was recovered from Terminal Dogma. He would be cremated, the ashes disposed of. Not even an unmarked grave would suffice, not after the truth behind Second Impact was revealed during the battle, thanks to Otacon and Mei Ling.

The Patriots had also lost one of their own. Whilst leading the defense of the Geofront, Ocelot was injured, having been shot several times. He was immediately evacuated to Nerv's medical wing. Despite Naomi and Ritsuko's best efforts, there was no hope for Ocelot.

Big Boss rushed to his friend's side once the news was known. He found Ocelot in a guarded room, lying on a cot, looking the worse for the wear.

Big Boss grasped Ocelot's hand tightly. "Ocelot."

"Did we win?" Ocelot asked.

Big Boss nodded. "Yes. We won, old friend. Third Impact will never come to pass. You have done your duty well."

Ocelot smiled weakly. "Thanks, Boss." He was fading fast. "It...it was a honor...to have died by your side..."

"And it was an honor to have fought by yours. It's time to put the gun down and rest, Adamska. You have earned it."

Ocelot's grip increased as he fought for breath. Then he breathed his last, his grip going slack in Big Boss' hand. The old man reached over and closed Ocelot's eyes.

The war was finally over, but there was the matter of Seele, more importantly, Zero. There would be nowhere for Seele to hide, since Otacon and Mei Ling were in the process of blowing the lid off of Second Impact. By this time tomorrow, the whole world would know the truth, as well as what had happened in the city of Tokyo-3. The heroes would be remembered, the villains cursed and damned.

But Big Boss wasn't finished. There was still one loose end to tie up.

And thanks to Otacon and Mei Ling, he knew where Zero was hiding.

* * *

Location - ?

"Shinji...Shinji..."

All Shinji saw was blinding white. Then, his vision slowly came into focus. He was slumped up against a tree. Looking around, he saw that he was what appeared to be in a waterfront park. It took Shinji a moment, but he remembered this place from his memories.

The Lake Ahinoko Levy at Hakone.

It was shortly before the ill-fated 'Contact Experiment,' that his mother had brought him here when he was only four.

"Shinji..."

Shinji got to his feet and looked around. "Where am I? Am I dead?"

"Far from it, my son," the female voice said from behind him.

Shinji turned around. Standing before him was someone he had thought to have been dead for over a decade. A Japanese woman, in her late twenties, dark brown hair cut short in a mop, kind brown eyes. The white lab jacket partially concealed her pink blouse and black skirt.

"It's been a long time, Shinji," Yui Ikari said. "Far too long."

Shinji felt a lump in his throat. "M-Mom? Is it you?"

Yui nodded. "Yes. It's me."

That was all Shinji needed to hear. He rushed over and threw his arms around his mother.

"I've always been here," Yui said soothingly as she stroked her son's hair, hugging him back. "Always watching over you inside Unit One."

Shinji broke off the hug. "Unit One? But how?"

Yui smiled sadly. "I think I should start from the beginning," she said as she sat down in the shade of the tree. Patting to the space beside her, Shinji took a seat beside her. "Gendou never really talked about me as much, did he?"

Shinji shook his head. "Whenever I tried to ask him about you, he would refuse to answer. Most of the information I got about you was from Fuyutsuki."

Yui smiled. "The professor always had a soft spot for me. I was his best student, after all." Her smile faded. "I promised you an explanation, and I am a person of my word. Have you ever wondered why the Angels continued to attack Tokyo-3, or about the origins of the Evangelions?"

"Both."

Yui smiled. "You are definitely my son. It was in the years following Second Impact. Gendou and I worked for Nerv's predecessor, Gerhin. He was the commander of the Geofront, while I was the Chairwoman of Project E, the post that is currently being held by Ritsuko Akagi. The reason being as to why the Angels kept attacking Tokyo-3 is because there is an Angel hidden in the Geofront."

"An Angel?"

[Cut to a shot of Lilith, hanging on her cross, with the Lance impaled through her.]

YUI (voice-over): Not just any Angel, Shinji. Lilith, the Second Angel, and progenitor to the Lilim. In other words, she is the mother to humanity, whereas ADAM was the progenitor of the Angels.

SHINJI (voice-over): Are you telling me that humanity is descended from Lilith?

YUI (voice-over): Yes. In a matter of speaking, humanity, or Lilum, is the Eighteenth Angel.

SHINJI (voice-over): Ritsuko mentioned that humanity and the Angels had the same type of DNA.

[Shots of the Angels, from Sachiel to Tabris.]

YUI (voice-over) The Geofront itself is Lilith's Black Moon, having crashed here over four billion years ago. Lilith had arrived shortly after ADAM, and since two Seeds of Life could not coexist on the same planet, ADAM went into hibernation, and humanity was allowed to flourish.

SHINJI (voice-over): The Angels were attacking Tokyo-3 because they thought Lilith was ADAM. What about the Evangelions?

[Shots of Units Zero through Two in action.]

YUI (voice-over): You thought that the EVAs were just mere mecha as seen in anime? They are much more than that, Shinji. Evangelion is nothing more than a giant human being of near godlike power, cloned from ADAM and Lilith. Your Unit One and Ayanami's Unit Zero were cloned from Lilith, while Sohryuu's Unit Two was cloned from ADAM. The armor plating served as restraints to help control them. It was a trial-and-error process, but we managed to perfect the process of creating the Evangelions in order to combat the Angels.

SHINJI (voice-over): Unbelivable.

YUI (voice-over): The first three EVAs had a critical flaw. The cores were not Super Solenoid engines, and would not work under normal circumstances. Sadly, I was the first to figure out how the EVAs could function. Kyokou was the second.

[Clips end here.]

"Kyokou?" Shinji parroted.

"Kyokou Sohryuu, also a researcher in the Evangelion project, and Asuka's mother," Yui explained. "The EVAs could only function with the power of a human soul. It was also selfish of me, but my own life was in danger."

"By who?"

"Your father. It was after you had turned four that I had discovered Gendou's role in Second Impact. My father - who sat on the council of Seele - confirmed it." Off Shinji's shocked look, Yui continued. "Yes, son. Your grandfather, my father, was part of Seele. In fact, he was the only one who had voiced opposition in unleashing Second Impact. I think that was one of the reasons why Gendou was attracted to me."

"Because of your connections to Seele?"

Yui nodded. "Yes. Shinji...I owe you an apology. When I found out your father's role in Second Impact, I suspected that if he was able to sabotage an experiment with ADAM and cause the deaths of over three billion people, then he would not think twice in killing me, or harming you. That was when I found out about EVA's flaws with the core...and I volunteered with the Contact Experiment. There was something that Gendou did not know about Unit One. It would not accept female pilots, since Unit One was cloned from Lilith herself."

Shinji connected the dots. "You allowed yourself to be absorbed into the core in an attempt to keep yourself safe from Gendou."

Again, Yui nodded. "Yes, son. And ever since the Angel Wars, I've been there, protecting you in any way I could."

Shinji searched his memories. He remembered Unit One protecting him from falling debris during the battle with Sachiel, as well as the EVA going nuts on said Angel and Zeruel as well.

"So that was you making my EVA going berserk?"

"That was me."

"So Kyokou lost her mind because Unit Two was cloned from ADAM, and Unit Two would only accept female pilots, right?"

"You catch on quick. You're definitely my son."

Shinji smiled. "So what happened after you were absorbed into the core?"

"Dad lost it," Yui replied sadly. "You only met him a couple of times, Shinji. You were still very young. But he liked you. When he thought I died, he committed suicide out of grief. I heard that Gendou was the one ordered to kill him." She looked out at the lake. "Here, I thought Gendou actually loved me. Now, thanks to you...I finally see the truth."

"Fuyutsuki told me about Gendou's plans," Shinji continued. "He told me shortly before Arael. That sounds a whole lot like obsession if you ask me. But I think that the old bastard wanted to become a god, to mold and shape the world as he saw fit."

"Perhaps..."

Shinji was silent for a moment. "So what happens now...? Can we get you back?"

Yui shook her head. "Sorry. You were a special case. Me...I can't get out of the core. I'm sorry, Shinji. But you do have friends that care for you on the outside."

"I know. I know that now. So what happens to the EVA?"

[Another fade out. This time, it's a clip from End of Evangelion. Unit One is out in space, with the Lance of Longinus.]

YUI (voice-over): Fuyutsuki once asked me as we developed the EVAs is it mankind's desire to become God? To create a being of nearly ominpotent power in order to obtain immortality?

SHINJI (voice-over): What did you tell him?

YUI (voice-over): I told Kouzou that humans can live on Earth, but the Evangelion can live forever...together with the human soul that lives within its core. Even when the Sun, the Earth, and the moon vanish into history, the Evangelion will exist even as a single person still lives. It will be lonely, yes, but as long as that person still lives, it will be the eternal proof that mankind ever existed.

[Clip ends here.]

Yui turned towards Shinji. "Shinji...what you have done here...by stopping Seele's ambitions for Human Instrumentality...you have shown that mankind is not beyond redemption. Mankind will survive, and continue to rebuild."

Shinji watched as she began to rise into the air. "Mom! Mom, wait!"

"I wish we had more time to spend together," Yui said as she rose out of reach, "but it's time for me to go." She reached into her pocket and pulled out a locket. Tossing it to Shinji, who caught it, she said, "Something to remember me by. Goodbye, Shinji Ikari...and good luck..."

As Yui floated away, Shinji opened the locket. Inside was a picture of Yui, along with a 4-year-old Shinji. A single tear ran down Shinji's cheek as he closed the pendant and held it close.

"Goodbye...Mother..."

* * *

January 1, 2016 – three days after the Battle of Tokyo-3.

Nerv Headquarters, the Geofront.

Shinji Ikari opened his eyes. 'Great. Another unknown ceiling,' he thought. Then his vision slowly came into focus. 'Wait a second...this is the medical facility inside the Geofront.'

The last thing Shinji remembered before passing out was beating Asuka to within an inch of her life, followed by Kaji and Misato running over to him as he lost consciousness.

"You're finally awake, Shinji."

It was at that moment that Shinji had noticed Rei in the chair next to his bed. Rather than her school uniform or even her plug suit, she was dressed in a simple workout suit, similar to what Touji would wear, save that hers was dark blue. Shinji also noticed that her hand was clasping his uninjured one.

"Rei," Shinji whispered. "How long was I out?"

"Three days," Rei replied. "Today is the New Year, 2016."

"So...we survived Third Impact?"

"Third Impact has been successfully averted. ADAM has been destroyed, and Terminal Dogma has been sealed." When Shinji tried to sit up, Rei stopped him. "No, Shinji. You must rest. You were injured following your fight with Sohryuu."

"How bad was I?"

"Four broken ribs, a fractured wrist, a fractured eye socket, three broken fingers, and a nasty concussion," Rei replied. She pointed to the IV in his arm. "Doctor Akagi had you placed on insulin in order to provide you with nutrients for your body."

"So...what happened?" Shinji asked.

"As of this moment, Nerv is under control of the Japanese Government. The Japanese Strategic Self-Defense Force has been occupying the Geofront as well as Nerv Headquarters. Commander Fuyutsuki, Doctor Akagi, and Lieutenant Colonel Katsuragi are currently being debriefed by the Prime Minister, as well as the Secretary General of the U.N. The whole world knows about what Gendou and Seele were planning."

"What happened to Gendou?"

"Dead. Katsuragi and Akagi shot him during the battle. He died in Terminal Dogma. Prior to that, he was stripped of his duties as the Supreme Commander of Nerv."

It was then Shinji noticed that someone was missing. "Wait. Where's Big Boss?"

"He left shortly after the battle was over," the blue-haired pilot of Unit Zero replied. She smiled. "I'm glad that you are safe, Shinji." She then leaned in and kissed him softly on the cheek. "Get well soon."

The kiss sure as hell caught Shinji off guard. But it was more welcomed than a slap. And Rei hit as hard as Asuka. "Wow. A kiss from you, Wondergirl? First you slap me, now you kiss me."

Rei smiled shyly. "Let's just say that you are improving in my eyes." She then left the room.

Shinji watched her leave. He then noticed the object that was around his neck.

A locket, belonging to his mother.

Shinji opened it, and regarded the picture of himself and his mother for one long moment, holding it close to him, fresh tears running down his face.

* * *

Several hours later, the newly-appointed Commander Fuyutsuki and Colonel Katsuragi visited Shinji. He was being checked out by Naomi, who decided to stay behind to help tend the many wounded that were left following the battle. Ritsuko Akagi was down the hall, briefing the JSSDF medics and several doctors.

The old man and the ponytailed colonel gave further detail into what was going on. As it turned out, FOXHOUND had several UAV drones in both the Geofront and the city above, which had taped the entire battle, including the battle between him and Asuka.

As it had also turned out, Asuka's eye was damaged as a result of her high synchronization, and in the final battle between herself and Shinji, he had damaged it to the point that she could never see out of it again. After she had gotten her eye treated, she was shipped off to the World Court in The Hague to face charges of crimes against humanity.

The Nerv bridge crew, the JSSDF and the U.N. crack troops that had participated in the battle were looking at several serious awards and recommendations. Since Shinji and Rei were both employed with Nerv, and by an extension, the United Nations, both were warrant officers – a little tidbit that Gendou had failed to mention, both were also being hailed as heroes for their role in preserving humanity.

"Your mother would be proud of you, Shinji," Fuyutsuki said, smiling. "I know I am."

"We all are," Misato added. "You did good, Shinji."

"Indeed," Naomi concurred. "Big Boss left shortly after the battle, said that he had some loose ends to tie up. But he did left you a message. He said that you did good, and that he is proud of you. As am I. But don't let it go to your head, Ikari."

"Trust me. I won't. Can you do e a favor, Commander?"

"Anything."

"Remove my mother's last name from Gendou's. I don't want her legacy tainted by that bastard."

Fuyutsuki nodded. "Done."

With his mother effectively separated from that bastard, there was something else that was nagging Shinji. "Fuyutsuki...what happened to Unit One?"

Misato and Fuyutsuki exchanged glances. Even Naomi went silent. After a moment, Fuyutsuki spoke. "It's gone, Shinji. Along with the Lance of Longinus. It happened shortly after the battle. The Japanese government had decided that the EVAs were too dangerous to keep around, and had ordered them to be destroyed. Unit Zero was the first, as was Unit Five. When it came for Unit One to follow suit, it activated on its own. The Lance of Longinus, which we kept down in Terminal Dogma, appeared and they both...disappeared."

"Nobody knows where Unit One is," Misato concluded.

Shinji smiled a little smile. He had a good clue as to the fate of his EVA, and more importantly, his mother. "'Even when the Sun, the Earth, and the moon vanish into history, the Evangelion will exist even as a single person still lives,'" he quoted.

Fuyutsuki nodded. "Your mother said that at Lake Ahinoko." He turned to Misato. "Call the Prime Minister and the Secretary General. Tell them that Unit One is no longer a threat."

Misato nodded. "Commander."

Once Misato was gone, Fuyutsuki gave Shinji a pat on his head before leaving. Shinji turned to Naomi. "When will Big Boss come back?"

"As soon as he ties up some loose ends," Naomi replied as she resumed her checkup on Shinji. "He has unfinished business to take care of."

* * *

The Rock of Gibraltar – January 5, 2016.

A week has passed since the climatic battle in Tokyo-3. Third Impact and Instrumentality had been successfully averted. Seele has forever lost their chance for immortality. Not that they had long to live for, anyway.

Thanks to The Patriots, the truth behind Second Impact, as well as Seele's intentions for Third Impact and Human Instrumentality had become known to the world. Forty-eight hours following the Battle of Tokyo-3, the world governments took action. Warrants were issued for the arrests of the surviving members of Seele and their supporters. Out of the seven surviving members of the mysterious cabal, three were lynched by the angry mobs, while the other three were held in protective custody.

Which leaves the leader of Seele, who was the mastermind behind Second Impact, as well as the scheme that would have all but finished what Second Impact had begun.

David Oh, alias Zero, alias Keel Lorenz.

Ever since returning from Old Tokyo following its destruction, Zero had not once left the safety of his mountain compound. With the rest of the world hunting him down, as well as arresting any and all Seele members and operatives, Zero remained safe inside his mountain home.

Until today.

Zero was inside his office, a mirror copy of the same one he had years earlier when he was in charge of The Patriots. Zero knew that Seele was finished, and that Big Boss would soon come for him.

**KA-CHAK.**

Zero showed no response or reaction upon hearing the sound of a certain modified machine gun being armed. The ancient man remained at his desk, hands clasped together.

"Modified Colt XM-16E1," Zero said. "I've been expecting you, Jack."

Big Boss stepped from the shadows, the aforementioned gun in his hand. His face was a grim line as he looked at the man he once considered his closest friend. "Zero," he growled.

Zero leaned back in his chair. "I underestimated you, Jack. You were never one to quit. The victory is yours."

"You seem pretty calm for someone who is about to die," Big Boss sniped.

Zero smirked. "Oh, I will not be the one who will die today," Zero said as he pressed a button on his desk.

Nothing happened.

Zero pressed the button several more times, and got the same result each time.

"Expecting your hired muscle to save your skin?" Big Boss asked, enjoying the shocked look on Zero's face. "Your hired muscle was the first thing my team and I had eliminated. Had to go through two silencers and four clips of ammo. But it was worth it. My son and his friends are laying waste to any stragglers. Gotta love stealth camo."

Zero knew that he was screwed.

Big Boss caught the expression on Zero's face. "What can I say? This fox is one step ahead of the hounds," he said, using Zero's words against him. "It time to face your crimes, Zero. You will not live to see The Hague."

As Big Boss raised The Patriot, Zero had asked, "So...you're my executioner. Does the condemned get one last wish?"

"No," Big Boss flatly replied, right before pulling the trigger, the faces of EVA, Revolver Ocelot, Roy Campbell, The Sorrow, and The Boss flashed into his mind. He didn't stop for one full minute.

By that time, Zero was dead, bullet holes in his head and chest, his body bleeding out, the armor-piercing rounds doing their job.

Big Boss lowered the gun and reached into his pocket. Retrieving a white phosphorous grenade, he pulled the pin and tossed it onto Zero's body. Seconds later, the grenade detonated, and the desk, along with Zero's body, was consumed in the flames.

Big Boss pulled out several more phosphorous grenades and tossed them across the room. He proceeded to do this in key area around Zero's hideaway.

By the time Big Boss had exited the mansion, it was completely engulfed in flames. Bodies of Zero's guards littered the walkway from the house to the helipad, where a Philanthropy chopper waited. In the pilot seat, was Otacon. Along for the ride, were Solid Snake, Meryl Campbell and Raiden. All three were armed, and had taken out any stragglers left behind in Big Boss' wake. Only two of Zero's men had the common sense to surrender, and thus, were spared.

The old man boarded the helicopter, and closed the door behind him.

Snake looked at his father. "Well?"

"It's finished," Big Boss replied as the chopper lifted into the air. "Zero is no more. Seele has been completely destroyed."

"So what happens now?" Meryl asked.

"As of this moment...the Patriots are now disbanded," Big Boss replied. "Saving humanity...that was my final mission. I think I'm overdue for a nice long retirement. As for the both of you...you're now free to make your destiny."

Big Boss said nothing else as Zero's hideout burned to the ground, the chopper flying away from the wreckage. He leaned back in his seat and closed his eye as sleep finally came to him.

His war was finally over. He was now free of his past.


	11. Episode 10: The End of Evangelion Gear

Episode 10: Epilogue, or The End of Evangelion Gear

Snafu's Notes: Here it is, folks. The final chapter of Evangelion Gear. Got to admit that it was one hell of a ride, but all good things must come to an end. Even I was impressed with the positive response from the readers as a result of writing this piece. Truthfully, I wasn't expecting for this to go as well as it had. From the bottom of my heart, I thank you.

One more thing. **Bold text** denotes Shinji narrating.

Without further ado, the conclusion to Evangelion Gear.

[The screen is blank. We see the following caption: **AD 2000 – September 13**, followed by ADAM's Wings of Light over the South Pole. Throughout this episode, an older Shinji Ikari is narrating.]

SHINJI: **In the early 21st Century, a cataclysmic event had forever changed the history of mankind. Second Impact. Two billion lives ended in the mega-tsunamis that enveloped the Southern Hemisphere. The weather patterns shifted, the Earth thrown off its axis, reducing the world to a permanent summer. Another billion people would die in the ensuing wars, plants and animals were rendered extinct as a result.**

[Screen goes blank again. Now the caption reads **AD 2015**. We see clips from Neon Genesis Evangelion, and various scenes from Evangelion Gear, most of them have Shinji in them.]

SHINJI: **Fifteen years later, I was called to Tokyo-3 to pilot the Evangelion. Cloned from the DNA of Lilith, the Progenitor of mankind, Unit One, along with Unit Zero and Unit Two, defended humanity against the Angels in what is now known as the Angel Wars. My name is Shinji Ikari, and this is my story.**

[Now the caption reads **AD 2031 – August 27. Present Day**.]

A car is driving up the road. Inside the car is three people – a family. The woman is behind the wheel, dressed in a simple white blouse and knee-length black skirt. Her cobalt-blue hair, pale skin, and crimson eyes are a dead giveaway as to who she is. A wedding ring – a simple gold band with a diamond on it – is on her ring finger.

The passenger is her husband. He is dressed in a simple black suit, with white shirt, the top buttons undone. His hair is the same it has been when he was a teenager, only shorter. A wedding band was on his finger. In the back seat, fast asleep, was their daughter, about eight years old, with the pale skin of her mother, and the dark hair and cobalt eyes of her father. It is pretty obvious that the couple is Rei Ayanami, now Rei Ikari, and Shinji Ikari, 14 years older.

Shinji is looking out the window, lost in his thoughts. Shinji glances at Rei, smiling briefly before going back to looking out the window.

SHINJI: **Fourteen years. Can't believe it's been that long since I was a kid. Seemed like a lifetime ago. I guess I should start on the day after the war. The battle would be known to future generations mostly as the Battle for Humanity. Bug for those who actually fought, it was known by another name. Given its location, it was also known as the Battle of the Black Moon.**

[Shot of a younger Shinji and Rei together, in the aftermath of the Battle of the Black Moon.]

SHINJI: **I guess it started with that first kiss Rei gave to me when I was recovering from the fight with Asuka. On Commander Fuyutsuki's orders, she moved out of that run-down apartment she was staying in, and moved in with Misato and I.**

[Tokyo-3 Junior High School. Shinji and Rei are greeted with applause from their classmates. Kensuke is filming the entire thing, while Hikari and Touji welcome him back to the class. Later on, they are on the rooftop, eating lunch alone. Rei is smiling. She is enjoying her time with Shinji.]

SHINJI: **We started to grow closer following the war, something that Gendou would have frowned upon when he was alive. Aside from that, as I later found out when I was cleared to return to school, aside the fact that I was transferred back into Class 2-A, that Rei and I were considered heroes, and rightfully so. By the end of the school year, we had begun dating. Touji and Kensuke were shocked as to me dating Rei. Of course, Touji, in turn hooked up with Hikari, and Kensuke found himself a female otaku of his own. Both got married, and we're still friends to this very day.**

[A snapshot of Shinji and Rei, on the couch, asleep. Obviously Misato's handiwork.]

SHINJI: **Misato had a field day when she found out that Rei and I started dating. When Rei decided to sleep in my room, I thought I'd never hear the end of that. But in the end, Misato decided to let it be. Of course, that didn't stop me and Rei from having a couple of makeout sessions behind closed doors.**

[Another snapshot. This time, it's Shinji and Rei, several years older. It's a wedding photo. Shinji is in his tuxedo, Rei is in her wedding dress. It's followed by video footage of their wedding, obviously shot by Kensuke.]

SHINJI: **We had gotten married after high school. Misato was the maid of honor, Fuyutsuki gave Rei away. Even Big Boss attended, along with Snake, Meryl, Otacon and Naomi. I heard that Snake had gotten hitched to Meryl about a year after the battle. Meryl still kept her last name. Rei, on the other hand, had taken mine. I work as a professor at Tokyo-3 University. Rei also works there alongside me.**

[Back to the present. Shinji looks in the backseat, where the product of his and Rei's union is fast asleep, snoring gently.]

SHINJI: **The little girl that's fast asleep is the product of our union. Aya Yui Ikari. Funny how things work out. Ritsuko had taken me to the side and had told me about Rei's origins, that she was unable to bear children. I guess her Angel side had reconstructed her womb, allowing her to become pregnant. Either way, being a dad is one of the many joys I have in my life.**

SHINJI: **I know what you're thinking. What the hell happened to Asuka? Well...**

* * *

[Fade out to another caption. **A.D. 2016 – March 29, three months after the Battle of the Black Moon**.]

U.N. War Crimes Tribunal, Tokyo-2.

Asuka Sohryuu was the first to be tried in her role in the Battle of the Black Moon. During the trial, Naomi was called up to testify on Asuka's psychological state during the Angel Wars. It was also revealed that Nerv Germany had knowledge of Asuka's mental problems, but did nothing, as they felt that it would affect her piloting. They simply swept her problems under the rug and said nothing.

The once-proud redhead stood in front of the trio of judges. She was dressed in a blue prison jumpsuit. As it had turned out, her left eye had been damaged beyond repair. The damaged eye was no longer a vibrant blue, but rather a solid white, like a zombie. Her red hair was tied back into a ponytail, the bangs covering her eyes, as her head was bowed low. Her wrists were shackled, as were her ankles, the latter being added when she tried to rush at Shinji several days earlier.

Right now, Asuka had just been found guilty by the U.N. tribunal. Also present were the senior members of Nerv – Commander Fuyutsuki, Colonel Katsuragi, Ryouji Kaji and Doctor Akagi. Even Shinji Ikari and Rei Ayanami were present for the sentencing.

SHINJI:** As it turned out, Nerv Germany had knowledge of Asuka's inferior complex, as well as her growing signs of becoming a sociopath. But they simply stood by and did nothing. Their crimes were exposed during Asuka's trial, and would get theirs soon.**

The senior judge looked down at the disgraced halvsie pilot. "Asuka Langley Sohryuu, you have been found guilty for the crime of treason, as well as the crime of being an accessory to Seele's plans for genocide. These charges carry an automatic death penalty. However, given the testimony of Doctor Hunter, as well as those in Nerv Germany in regards to your mental condition, you will not be sent to the firing squad. You will instead be sent to a mental hospital for the remainder of your natural life, never to be released."

"What?" Asuka shouted. "You old bastards! You can't do this to me! Do you know who I am? I'm Asuka Langley Sohryuu!" Two muscular guards grabbed her by the arms as she struggled violently, but was restricted by her shackles. "Let go of me, you glorified Boy Scouts! Damn it! I said let me go!"

"Remove the defendant," the judge ordered.

Turning her head so she could face Shinji and the others, she directed her threats towards Shinji. "DAMN YOU, SHINJI! THIS IS YOUR FAULT! ALL YOUR FAULT! YOU FUCKING RUINED MY LIFE!"

She was dragged out of the courtroom through a side door, still screaming. It would be the last time anyone from Nerv would see Asuka Sohryuu ever again.

SHINJI: **Now that I think about, I kinda feel sorry for Asuka. Being manipulated the way she had been, by both Nerv and Keel. Whether or not she hated me or feared me...we'll never know. One thing for certain is that she will be remembered, but not as the savior of humanity. But rather as a person who had sided with Seele in order to destroy the world.**

[Shot of a nude Asuka Sohryuu in her cell. She has hanged herself inside her cell, using her bedsheets as a noose. A mirror image of her late mother.]

SHINJI: **We received word regarding Asuka's fate. Four years into her life sentence she had begun an with her therapist. However, he was just using her for sex, as Gendou did with Ritsuko. When Asuka found out that he really didn't love her a year later, she flipped. She would be found the next day, having used her bedsheets as a noose. She was only nineteen. I actually shed a tear in regards to her suicide. She should have received some help in regards to her inner demons. But it's too late. Unlike her mother, she was buried with only her ID number identifying her and her date of death. The therapist was cleared of any wrongdoing...although when asked about it by his friends, he did say that 'she was the best piece of ass he ever had.'**

[Shots of the U.N. Inquiries. Misato Katsuragi, Kouzou Fuyutsuki, Ritsuko Akagi are testifying before the committee. Even Shinji Ikari and Rei Ayanami are summoned and questioned by the committee.]

SHINJI: **Asuka's trial was just one of many. The surviving members of Seele, as well as the Haven Shock Troops were tried, found guilty, and sentenced to death. The saying does ring true. The past really does catch up to you. Once the war crimes tribunal was finished, the U.N. inquiries about what was going on inside Nerv had begun. We were all summoned to testify, including Rei. As for Fuyutsuki and Ritsuko, Big Boss was true to his word. Both were granted immunity from prosecution. Misato was never charged with any wrongdoing. Rei and I were in the clear. As an added bonus for basically saving mankind, the U.N. gave all of us a nice pension as a way of saying thank you...not to mention the awards and praise from every world leader known to man.**

[Shot of the Nerv Insignia.]

SHINJI:** After the UN investigation into Nerv which lasted a full year, the United Nations had Nerv disbanded. The headquarters in the Geofront was converted into a biomedical research facility, Terminal Dogma remained forever sealed. Ritsuko Akagi was made the senior researcher of the facility. Kouzou Fuyutsuki, in the meantime, had retired and returned to Kyoto to be closer to his grandchildren and great grandchildren. The three bridge bunnies, Aoba, Hyuuga, and Maya, also remained at the Geofront, assisting Ritsuko in her research. Mei Ling decided to stay in Japan, where she and Makoto connected.**

[A picture of Ritsuko, circa 2030. She's dropped the bottle blonde look. She's also seen in the photo with another man.]

SHINJI: **Last I heard from Misato, she was seeing a JSSDF veteran who had fought inside the Geofront. Turns out he's also a cat lover. They haven't married, but they got a cute little girl together.**

[Shot of Maya and Aoba making out...and getting caught by Ritsuko.]

SHINJI: **Contrary to popular belief, Maya was not a closet lesbian as most people thought. Turns out that she and Shigeru were secretly dating. With Nerv disbanded and Gendou burning in hell, they were free to bring their relationship out into the open.**

[Shot of Misato and Kaji.]

SHINJI: **Speaking of relationships, Misato and Kaji had reconciled following the war. They got hitched shortly after the inquiries were complete Misato had resigned her commission with the United Nations and became a spokeswoman for Yesibu. Figures. Kaji decided to quit the spy game and settled down as well. He got a job working with the government, helping displaced children.**

[Shot of Pen-Pen...with a female hot springs penguin.]

SHINJI: **Turns out that Pen-Pen wasn't the only hot springs penguin. Misato found a female penguin that Pen-Pen took a liking to. Last I heard, they were still in Misato's care. I'll bet her and Kaji's children sure love their pet penguins.**

[Hal Emmerich and Naomi Hunter, as seen in MGS4, including the part where she yanks him inside the helicopter inside the Nomad.]

SHINJI: **After things had settled down, Naomi returned to America with Snake and the others. Now I know why she had shot down most of the men inside the Geofront, Gendou included. She was romantically involved with Dr. Emmerich. Have been since the Manhattan Incident of 2009. Naomi and I still talk. Mostly by trading e-mails. Sometimes, she visits Big Boss twice a year, and we all sit down and swap stories.**

[Shot of Solid Snake...or rather, Iroquois Pliskin and Meryl Campbell.]

SHINJI: **As it turned out, that little flaw in the Les Enfant Terribles in which Snake could not give Meryl children was nothing but a lie. Meryl, on the other hand, couldn't be even more happier. After FOXHOUND had disbanded, Snake and Meryl had decided to make it official. It was after the battle inside the Geofront, that Big Boss had given Snake some useful advice. "Never pass up on a good thing." Big Boss showed me the wedding photos.**

[Shots of Big Boss, from the story. Training Shinji...beating down Gendou's Section 2...confronting Snake and Meryl in Prague...saluting The Boss' grave alongside Ocelot.]

SHINJI:** As for the man who saved my life when I was at my lowest...he retired from the military a second time. Since then, he has written his memoirs. You may have read them. 'Memoirs of a Patriot: The Declassified Story of Big Boss.' It was number one on the bookseller's list for two years when it came out.**

[Shot of Big Boss entertaining Misato, Shinji, Rei, Kensuke, Kaji and Hikari with one of his many war stories.]

SHINJI: **You can imagine that Kensuke had a field day when I invited him over to the lodge, along with Touji and Hikari. Rei and Misato sometimes came along with me, and knew what to expect. To my friends, it answered the question about how I was able to defend myself against Asuka. Of course, I still got my ass kicked by the old man.**

* * *

[The caption now reads **Hakone Cemetery, AD 2020 – August 29**.]

SHINJI: **It happened five years following the Angel Wars. I was visiting Big Boss at his home when he collapsed. I called for an ambulance, and he was rushed to the hospital. The doctors had no explanation as to what had happened. But one thing was for certain. Big Boss, the man who saved my life, was dying. I called Snake, who immediately was on the next flight to Tokyo-3 with Meryl. Despite the doctor's best efforts, there was nothing that they could do. So we took Big Boss home, back to his lodge. 'To ride this storm out,' he said. But I guess even he knew that his end was near. And like a soldier, he saw it through to the end. In the face of his death, he did had one final request. He wished to die by EVA's grave.**

It was late in the afternoon as two cars pulled to a stop in Hakone Cemetery. In the front seat, was Big Boss. Solid Snake was behind the wheel. In the back seat, were Shinji Ikari, Rei Ayanami and Meryl Campbell. In the second car, were Hal Emmerich, Naomi Hunter, Misato Katsuragi and Ryouji Kaji. The old man was dressed in his FOXHOUND uniform and trenchcoat, the eyepatch ever still present on his face. Rather than the vibrant man that had helped saved humanity four years ago, there was just an old man who was simply tired.

When asked why he decided to dress up, Big Boss replied, "If this is my time, I wish to die in my best."

The small entourage got out of the cars, Snake and Shinji helping Big Boss down the pathway towards EVA's grave, as the others followed them.

"Boss...are you sure this is what you want?" Shinji asked.

"Yes, Ikari," Big Boss replied. "I appreciate your concern for me, but this old man's had his last tour." He coughed violently. "It's almost time. The last ember of the past dies out. And at last those old evils will be gone. Once the source of evil returns to zero. A new one...a new future will be born."

Within several minutes, the group of survivors stood before EVA's grave, the headstone still the same as it was when Big Boss buried EVA. The old man shrugged off his two crutches in order to stand at his companion's grave.

"I wish I could have told you more about your mother, Snake," Big Boss admitted. "She was something. Strong, resourceful, a speed demon on a bike and a hell of a shot with a Mauser." He crouched down at EVA's grave, one gloved hand running across the name. "Tatyana...it won't be long now. Soon...we will be reunited, my love."

He tried to get back up onto his feet, but failed. Instead, he turned around and rested his body up against EVA's headstone. He didn't have long now. Looking at the faces of his entourage, Big Boss smiled. "Consider this my final lesson to you," he said. The old man turned to Snake. "Snake...or rather, David...listen and listen well. This new world that you helped save...is yours to live in. Not as a snake...but as a man." He turned to Shinji. "Know this, the both of you...we all fought a long, bloody war for our liberty. Zero and myself...Liquid and Solidus...we fought to free ourselves from nations, systems, and norms, and ages. But no matter how hard we tried, the only liberty we found was on the inside. Trapped within those limits."

After coughing, Big Boss continued. "The Boss and I may have chosen different paths. But in the end, we were both trapped inside the same cage... Liberty. But you...all of you. Each one of you has been given freedom. Freedom to be outside. Shinji...Rei...Meryl...Misato...Ryouji...Otacon...Naomi...none of you are nobody's tool now, nor are you are no longer a prisoner of fate. None of you are no longer seeds of war."

The dying old man reached into his jacket and pulled out a cigar. He tried to light it, but failed, the cigar falling to the ground. It was Snake that had made the save. He retrieved Big Boss' last stogie, and lit it up. After taking a puff, he handed it to Big Boss, who began to enjoy his last smoke. "Shinji...you were like a son to me. I was honored to have taken you as my student. Remember what I've taught you, and use it in your life. Understand?"

Shinji nodded. "I will, Big Boss."

By this time, the cigar was nearly finished. Big Boss blew out a plume of smoke. In his mind, he saw The Boss smiling at him. "Boss...you only need one snake...no...on second thought...I think the world would probably be better off without snakes."

The cigar was still in his hand as he looked at the people closest to him. A smile crept across his face. In the face of his mortality, he was content. "This...this is good...isn't it?"

With those words, John Hayter, codename Naked Snake, christened Big Boss, the greatest soldier to have ever lived and one of the saviors of humankind, closed his eye and breathed his last breath. The cigar fell to the ground, its embers having died out.

Naomi crouched down next to the old man and checked for a pulse. There was none. The look on her face had verified it when she turned to the others. "He's gone," she said softly.

Shinji was the first to break down in tears. Rei held him close as he sobbed into her shoulder. There was not a single dry tear amongst the group of survivors.

* * *

SHINJI: **The funeral procession started in the city, near where I had fought Asuka, and ended at Hakone Cemetery. Rei was at my side. We buried him next to EVA in the Hakone Cemetery as per to his request in his will, the same place where my mother's headstone was located. It seems rather silly that her grave is empty, but I still visit there, and let her know what has been happening in my life. I wonder if she is still there, inside the EVA, floating in outer space...**

The following scene is that of Big Boss' funeral, in the streets of Tokyo-3. The funeral scene rivals that of Mahatma Gandhi. A single JSSDF officer leads the procession, holding a portrait of Big Boss, followed by a combat unit of JSSDF soldiers marching in half-step.

They were followed by the survivors of the Battle of the Black Moon, both from FOXHOUND and Nerv. All were in black mourning attire.

Shinji Ikari was dressed in a formal suit – black of course. Rei was at his side, in a mourning dress. Beside him, were Raiden, Solid Snake and Meryl Campbell, all dressed in FOXHOUND uniforms, berets and trenchcoats. Rosemary, along with Sunny and young Jack, walked alongside Raiden. Behind Shinji and Rei, were Misato Katsuragi and Ryouji Kaji, the former in her formal Nerv uniform, and the latter also in a formal suit. Beside them, were Kouzou Fuyutsuki and Ritsuko Akagi.

Following them – also in their formal Nerv uniforms – were the three bridge bunnies: Maya Ibuki, Shigeru Aoba, and Makoto Hyuuga. Hal Emmerich, Mei Ling, Naomi Hunter and the four Beauties brought up the rear, the all dressed in mourning clothes.

The entire world stopped what they were doing and watched the funeral on T.V. Those that lived in the Hakone region of Japan lined the streets, paying respects to a man they never knew, but was responsible for stopping Third Impact and exposing the truth.

SHINJI: **I soon found how what had killed him from Naomi. Terminal cancer. He should have been dead when we first met. But Naomi had told him why he survived.**

[Cut back to Big Boss' lodge. As a younger Shinji looks on at Big Boss' pictures, Big Boss is inside his bathroom. He is jamming a syringe into his neck. He performs the same thing shortly after ordering 'Susanoo's Wrath' to be executed.]

SHINJI: **Big Boss was diagnosed shortly after the incident in Prague, in which his lover and his best friend was killed. Naomi's specialty was nanotechnology, and she used her talents to create a special kind of suppressants that kept Big Boss' cancer at bay. When he stopped taking the treatments, the cancer had came back with a vengeance. Naomi had given him three months. He held on for nearly four months. He wanted to live long enough to make sure than humanity would survive.**

* * *

Hakone Cemetery – Present Day.

The car containing the Ikari family pulled to a stop, where another car was parked in front of them. Rei placed the car in park and cut the ignition. Turning to Shinji, she said, "You go on ahead, love. I'll watch Aya."

Shinji nodded. He exited the car, holding two bouquets of flowers in his hands, and began walking up the same stone pathway Big Boss would walk when he was alive, when he would visit EVA. The leaves fell around him as he neared his destination.

Shinji saw that there were two people at his objective – a couple. The redheaded woman had turned from the white-haired man and was walking towards Shinji. Shinji recognized her instantly.

Meryl Campbell.

Forty-four years old and she was aging gracefully. The former executive officer of FOXHOUND recognized Shinji, and smiled. "Shinji Ikari. How you been? How's Rei and little Aya?"

"I'm good," Shinji replied, smiling back. "How are the kids?"

"Oh, driving poor Otacon up the wall," Meryl replied. "I see you're alone."

Shinji shook his head. "Not really. Rei is back at the car with Aya. Can't believe it's been eleven years since the old man passed."

"Well, he always had a soft spot for you, Shinji. You were his best student."

"I know. So how's things between you and Snake?"

Meryl smiled. "Oh, things are good. He has his moments. I'll go and say hi to Rei and Aya. I've held you up long enough."

Shinji nodded and Meryl walked off. Shinji turned to his destination. There stood the old man with the white hair and matching moustache, a mirror image of Big Boss himself. Instead of the Sneaking Suit, he wore a simple suit. He stood before the two graves, hands clasped together, head bowed.

"I knew you'd come, kid," Solid Snake (Old Snake would be more appropriate) said as Shinji stood by him.

"I always make time to pay my respects to the old man," Shinji replied, looking at the graves.

"As do I," Snake replied. "So how are you holding up? You took his death pretty hard."

"Wouldn't you?"

"Touche, Ikari," the clone/son of Big Boss replied. "I miss him too. The old man had his faults and flaws, but he was a good man...a good soldier...and a good friend."

Shinji remained silent for a moment. "I met him when I was still piloting the Evangelion. I was going through the worst time in my life. I thought that nobody didn't care for me. I was even prepared to take my own life. But Big Boss came. He listened to me, took me as a student, taught me about life. For that, I am truly grateful to have met him."

Snake smiled. "He always had that charisma about him," he admitted. "That kind of charm is what soldiers trusted in him. Trust in Big Boss, and you will make it out alive."

He turned to Shinji. "Shinji...the old man is at peace now. I know it's hard...but life goes on." He gestured to Shinji's wife and daughter, Rei chatting with Meryl. "There's the proof right there." He placed one hand on Shinji's shoulder, looking the younger man in the eyes. "Shinji...remember what the old man had said. We all have been given freedom. Free from our past sins. Free from our personal demons. The old man is at peace, Ikari. Honor his memory by just living a good life."

With those words, Solid Snake removed his hand from Shinji's shoulder, turned and walked down the pathway, heading back towards Meryl.

After Snake had took his leave, Shinji turned to the dual headstones. Both were made of black marble. The headstone on the left read **TATYANA HAYTER – May 15, 1936 – August 27, 2013**, while the one on the right read **JOHN HAYTER – July 11, 1935 – August 29, 2020**.

Shinji placed the flowers on both their headstones. As he rises to his feet, his vision catches something. Shinji gasps at what he sees.

(The guitar solo of 'Old Snake' begins to play.)

What he sees is his mentor, Big Boss. He is younger, but still sporting the eyepatch. Next to him, is EVA, also younger. Both are dressed in their respective gear from Operation Snake Eater. EVA has one arm linked with Big Boss. Both are looking at Shinji. They both wave at him, while Shinji smiles broadly at the pair, nodding his head in respect. Big Boss is at peace.

SHINJI: **Boss...you would be happy. How ironic that the world decided to shun war following what had happened here and reorganize into a United Earth Government. Your dreams...The Boss' dreams...of a word united, is now a reality. The armed forces of the world had been revamped into a peacekeeping force under the control of the UEG. All weapons of war were mostly destroyed, or put to better use. Because of what had happened here, the world had opened its eyes.**

A flock of birds distract Shinji. When he turns back to the pair, Big Boss and EVA are gone.

(Guitar solo of 'Old Snake' ends here.)

Shinji turns back to the headstones. Like Big Boss, he is at peace. A moment of inspiration comes to him. Normally, he would come, say a couple of words, and leaves, but this time, he has the ultimate form of respect for Big Boss.

He snaps to attention, as if he was in the military.

SHINJI: **Big Boss...I never really said thank you...for saving my life all those years ago.**

Shinji Ikari salutes Big Boss' grave.

SHINJI: **But I am forever grateful to you...for showing me how to live without fear.**

[Black screen. The credits begin to roll. Basically, it's a combination of credits from both Evangelion and Metal Gear. Here, we see the cast of Evangelion Gear (English Cast) as 'Komm, susser Tod,' from End of Evangelion (the song played during Third Impact/Instrumentality) plays The music then changes to the MGS4 end credits theme afterwards. The credits end at the title of the fanfic, EVANGELION GEAR, done up in the MGS4 title text, and hold. We hear footsteps. Then after a moment, they stop.]

REI (voice-over): Shinji...are you all right?

SHINJI (voice-over): I'm all right, Rei. I'm all right now. The old man is at peace.

AYA IKARI (voice-over): Papa! Papa!

SHINJI (voice-over): Hey, you. (rustling is heard, he is picking her up) Wow. You're getting heavy. Better enjoy it while you can, Aya.

AYA (voice-over): Why are we here, Papa?

SHINJI (voice-over): I came to pay my respects to a legend. He saved my life...a long time ago.

REI (voice-over): You never talked about Big Boss. Not even after the Angel Wars. Do you want to talk about it now?

SHINJI (voice-over): I guess now is a good time to start, isn't it? But I won't tell you how he died. I'll tell you how he lived.

END.

[A picture of Shinji Ikari appears, dressed up as Big Boss, saluting appears, with the following.]

**CONGRATULATIONS! YOU HAVE COMPLETED EVANGELION GEAR! YOU ARE HEARBY AWARDED THE TITLE OF BIG BOSS.**

Snafu's Notes: And with that, Evangelion Gear is complete. Hope you enjoyed it.


End file.
